Compositions, kits, and methods for identification, assessment, prevention, and therapy of breast cancer

ABSTRACT

The invention relates to newly discovered nucleic acid molecules and proteins associated with breast cancer. Compositions, kits, and methods for detecting, characterizing, preventing, and treating human breast cancers are provided.

RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.11/821,773, filed on Jun. 25, 2007 which, in turn, claims priority toU.S. application Ser. No. 10/177,293, filed on Jun. 21, 2002 which, inturn, claims priority to U.S. provisional patent application Ser. No.60/299,887, filed on Jun. 21, 2001; U.S. provisional patent applicationSer. No. 60/301,572, filed on Jun. 27, 2001; U.S. provisional patentapplication Ser. No. 60/306,501, filed on Jul. 18, 2001; U.S.provisional patent application Ser. No. 60/325,002, filed Sep. 25, 2001;U.S. provisional patent application Ser. No. 60/362,585, filed Mar. 5,2002; and U.S. provisional patent application Ser. No. 60/380,391, filedMay 14, 2002. The entire contents of each of the foregoing applicationsare expressly incorporated herein by reference.

FIELD OF THE INVENTION

The field of the invention is breast cancer, including diagnosis,characterization, management, and therapy of breast cancer.

BACKGROUND OF THE INVENTION

The increased number of cancer cases reported in the United States, and,indeed, around the world, is a major concern. Currently there are only ahandful of treatments available for specific types of cancer, and theseprovide no absolute guarantee of success. In order to be most effective,these treatments require not only an early detection of the malignancy,but a reliable assessment of the severity of the malignancy.

The incidence of breast cancer, a leading cause of death in women, hasbeen gradually increasing in the United States over the last thirtyyears. In 1997, it was estimated that 181,000 new cases were reported inthe U.S., and that 44,000 people would die of breast cancer (Parker etal, 1997, CA Cancer J. Clin. 47:5-27; Chu et al, 1996, J. Nat. CancerInst. 88:1571-1579). While the pathogenesis of breast cancer is unclear,transformation of normal breast epithelium to a malignant phenotype maybe the result of genetic factors, especially in women under 30 (Mild etal., 1994, Science, 266:66-71). The discovery and characterization ofBRCA1 and BRCA2 has recently expanded our knowledge of genetic factorswhich can contribute to familial breast cancer. Germ-line mutationswithin these two loci are associated with a 50 to 85% lifetime risk ofbreast and/or ovarian cancer (Casey, 1997, Curr. Opin. Oncol. 9:88-93;Marcus et al, 1996, Cancer 77:697-709). However, it is likely thatother, non-genetic factors also have a significant effect on theetiology of the disease. Regardless of its origin, breast cancermorbidity and mortality increases significantly if it is not detectedearly in its progression. Thus, considerable effort has focused on theearly detection of cellular transformation and tumor formation in breasttissue.

Currently, the principal manner of identifying breast cancer is throughdetection of the presence of dense tumorous tissue. This may beaccomplished to varying degrees of effectiveness by direct examinationof the outside of the breast, or through mammography or other X-rayimaging methods (Jatoi, 1999, Am. J. Surg. 177:518-524). The latterapproach is not without considerable cost, however. Every time amammogram is taken, the patient incurs a small risk of having a breasttumor induced by the ionizing properties of the radiation used duringthe test. In addition, the process is expensive and the subjectiveinterpretations of a technician can lead to imprecision, e.g., one studyshowed major clinical disagreements for about one-third of a set ofmammograms that were interpreted individually by a surveyed group ofradiologists. Moreover, many women find that undergoing a mammogram is apainful experience. Accordingly, the National Cancer Institute has notrecommended mammograms for women under fifty years of age, since thisgroup is not as likely to develop breast cancers as are older women. Itis compelling to note, however, that while only about 22% of breastcancers occur in women under fifty, data suggests that breast cancer ismore aggressive in pre-menopausal women.

It would therefore be beneficial to provide specific methods andreagents for the diagnosis, staging, prognosis, monitoring, andtreatment of diseases associated with breast cancer, or to indicate apredisposition to such for preventative measures.

SUMMARY OF THE INVENTION

The invention relates to cancer markers (hereinafter “markers” or“markers of the inventions”), which are listed in Tables 1-12. Theinvention provides nucleic acids and proteins that are encoded by orcorrespond to the markers (hereinafter “marker nucleic acids” and“marker proteins,” respectively). Tables 1-12 provide the sequenceidentifiers of the sequences of such marker nucleic acids and proteinslisted in the accompanying Sequence Listing. The invention furtherprovides antibodies, antibody derivatives and antibody fragments whichbind specifically with such proteins and/or fragments of the proteins.

Table 1 lists all of the markers of the invention, which areover-expressed in breast cancer cells compared to normal (i.e.,non-cancerous) breast cells. Table 2 lists markers identified bytranscription profiling using mRNA from 23 invasive ductal carcinoma(IDC) node negative breast tumors with good outcome and 16 IDC nodenegative breast tumors with poor clinical outcome. Table 3 lists markersidentified by transcription profiling using mRNA from 16 IDC nodenegative breast tumors and 19 IDC node positive breast tumors. Table 4lists markers identified by transcription profiling using mRNA from 25IDC node negative breast tumors with good outcome and 18 IDC nodenegative breast tumors with poor clinical outcome. Table 5 lists markersparticularly useful in screening for the presence of breast cancer(“screening markers”). Table 6 lists markers particularly useful inassessing aggressiveness of breast cancer (“aggressiveness markers”).Table 7 lists markers particularly useful for both screening breastcancer and assessing aggressiveness of breast cancer. Table 8 listsmarkers whose over-expression correlates with good clinical outcome,i.e., greater than 5 years of disease-free survival. Table 9 listsmarkers whose over-expression correlates with poor clinical outcome,i.e., less than 3 years of disease-free survival. Table 10 lists newlyidentified nucleic acid and amino acid sequences. Table 11 lists newlyidentified nucleic acid sequences. Table 12 lists staging markers whoseexpression correlates with metastasis to lymph nodes.

Tables 1-12 provide the name of the gene corresponding to the marker(“Gene Name”), the sequence listing identifier of the cDNA sequence of anucleotide transcript encoded by or corresponding to the marker (“SEQ IDNO (nts)”), the sequence listing identifier of the amino acid sequenceof a protein encoded by the nucleotide transcript (“SEQ ID NO (AAs)”),and the location of the protein coding sequence within the cDNA sequence(“CDS”).

The invention also relates to various methods, reagents and kits fordiagnosing, staging, prognosing, monitoring and treating breast cancer.“Breast cancer” as used herein includes carcinomas, (e.g., carcinoma insitu, invasive carcinoma, metastatic carcinoma) and pre-malignantconditions. In one embodiment, the invention provides a diagnosticmethod of assessing whether a patient has breast cancer or has higherthan normal risk for developing breast cancer, comprising the steps ofcomparing the level of expression of a marker of the invention in apatient sample and the normal level of expression of the marker in acontrol, e.g., a sample from a patient without breast cancer. Asignificantly higher level of expression of the marker in the patientsample, as compared to the normal level, is an indication that thepatient is afflicted with breast cancer or has higher than normal riskfor developing breast cancer.

The methods of the present invention can be of use in identifyingpatients having an enhanced risk of developing breast cancer (e.g.,patients having a familial history of breast cancer and patientsidentified as having a mutant oncogene). The methods of the presentinvention may further be of particular use in evaluating the specificstage of breast cancer, as well as in assessing whether the cancer hasmetastasized (e.g., metastasis to the lymph nodes). The methods of thepresent invention are also useful in predicting the clinical outcome fora patient with breast cancer, or for a patient who has undergone therapyto eradicate breast cancer. The methods of the present invention arealso be useful in assessing the efficacy of treatment of a breast cancerpatient (e.g., the efficacy of chemotherapy).

According to the invention, the markers are selected such that thepositive predictive value of the methods of the invention is at leastabout 10%, preferably about 25%, more preferably about 50% and mostpreferably about 90%. Also preferred are embodiments of the methodwherein the marker is over-expressed by at least five-fold in at leastabout 15% of stage 0 breast cancer patients, stage I breast cancerpatients, stage IIA breast cancer patients, stage IIB breast cancerpatients, stage IIIA breast cancer patients, stage IIIB breast cancerpatients, stage IV breast cancer patients, grade I breast cancerpatients, grade II breast cancer patients, grade III breast cancerpatients, malignant breast cancer patients, ductal carcinoma breastcancer patients, and lobular carcinoma breast cancer patients, and allother types of cancers, malignancies and transformations associated withthe breast.

In a preferred diagnostic method of assessing whether a patient isafflicted with breast cancer (e.g., new detection (“screening”),detection of recurrence, reflex testing), the method comprisescomparing:

-   -   a) the level of expression of a marker listed in Table 1 in a        sample from the patient, and    -   b) the level of expression of the marker in a control subject        not having breast cancer.        A significantly higher level of expression of the marker in the        patient sample, as compared to the level in the control subject,        is an indication that the patient is afflicted with breast        cancer. In one embodiment, the marker is listed in Table 5.

The invention additionally provides a diagnostic method for determiningwhether a patient has an aggressive breast cancer, the method comprisingcomparing:

-   -   a) the level of expression of a marker listed in Table 1 in a        sample from the patient, and    -   b) the level of expression of the marker in a sample from a        control subject having an indolent breast tumor or no breast        tumor.        A significantly higher level of expression in the patient        sample, as compared to the level in the sample from the control        subject, is an indication that the patient has an aggressive        breast cancer or is likely to develop an aggressive breast        tumor. No difference in expression between the patient sample        and the control sample, or a significantly lower level of        expression in the patient sample, as compared to the control        level, indicates that the patient has an indolent breast cancer.        In one embodiment, the marker is listed in Table 6.

The invention further provides a diagnostic method for determiningwhether a patient has breast cancer that has metastasized or is likelyto metastasize, the method comprising comparing:

-   -   a) the level of expression of a marker listed in Table 1 in a        sample from the patient, and    -   b) the level of expression of the marker in a sample from a        control subject having a non-metastasized breast tumor or no        breast tumor.        A significantly higher level of expression in the patient sample        as compared to the level in the sample from the control subject        is an indication that the breast cancer has metastasized or is        likely to metastasize. In one embodiment, the marker is selected        from the markers in Tables 6 and 12.

In another embodiment, the present invention includes a method fordetermining whether a patient has breast cancer that has metastasized tolymph nodes, or is likely to metastasize to lymph nodes, the methodcomprising comparing:

-   -   a) the level of expression of a marker listed in Table 1 in a        sample from the patient, and    -   b) the level of expression in a sample from a control subject        having a non-metastasized breast tumor or no breast tumor.        A significantly higher level of expression in the patient sample        as compared to the level in the sample from the control subject,        is an indication that the patient is afflicted with metastatic        breast cancer that has metastasized to lymph nodes, or is likely        to metastasize to lymph nodes. In one embodiment, the marker is        selected from the markers of Table 12.

The invention also provides a method for predicting the clinical outcomeof a breast cancer patient, the method comprising comparing:

-   -   a) the level of expression of a marker listed in Table 1 in a        sample from the patient, and    -   b) the level of expression of the marker in a sample from a        control subject having a good clinical outcome (i.e., a former        breast cancer patient having greater than five years of        disease-free survival level).        A significantly higher level of expression in the patient sample        as compared to the expression level in the sample from the        control subject is an indication that the patient has a poor        clinical outcome, i.e. less than 3 years of disease-free        survival. In one embodiment, the marker is selected from the        markers of Table 9.

The invention also provides methods for assessing the efficacy of atherapy for inhibiting breast cancer in a patient. Such methods comprisecomparing:

-   -   a) expression of a marker of the invention in a first sample        obtained from the patient prior to providing at least a portion        of the therapy to the patient, and    -   b) expression of the marker in a second sample obtained from the        patient following provision of the portion of the therapy.        A significantly lower level of expression of the marker in the        second sample relative to that in the first sample is an        indication that the therapy is efficacious for inhibiting breast        cancer in the patient.

It will be appreciated that in these methods the “therapy” may be anytherapy for treating breast cancer including, but not limited to,chemotherapy, radiation therapy, surgical removal of tumor tissue, genetherapy and biologic therapy such as the administering of antibodies andchemokines. Thus, the methods of the invention may be used to evaluate apatient before, during and after therapy, for example, to evaluate thereduction in tumor burden.

In a preferred embodiment, the methods are directed to therapy using achemical or biologic agent. These methods comprise comparing:

-   -   a) expression of a marker of the invention in a first sample        obtained from the patient and maintained in the presence of the        chemical or biologic agent, and    -   b) expression of the marker in a second sample obtained from the        patient and maintained in the absence of the agent.        A significantly lower level of expression of the marker in the        second sample relative to that in the first sample is an        indication that the agent is efficacious for inhibiting breast        cancer, in the patient. In one embodiment, the first and second        samples can be portions of a single sample obtained from the        patient or portions of pooled samples obtained from the patient.

The invention additionally provides a monitoring method for assessingthe progression of breast cancer in a patient, the method comprising:

-   -   a) detecting in a sample from the patient at a first time point,        the expression of a marker of the invention;    -   b) repeating step a) at a subsequent time point in time; and    -   c) comparing the level of expression detected in steps a) and        b), and therefrom monitoring the progression of breast cancer in        the patient.        A significantly higher level of expression of the marker in the        sample at the subsequent time point from that of the sample at        the first time point is an indication that the breast cancer has        progressed in the patient, whereas a significantly lower level        of expression is an indication that the breast cancer has        regressed.

The invention moreover provides a test method for selecting acomposition for inhibiting breast cancer in a patient. This methodcomprises the steps of:

-   -   a) obtaining a sample comprising cancer cells from the patient;    -   b) separately maintaining aliquots of the sample in the presence        of a plurality of test compositions;    -   c) comparing expression of a marker of the invention in each of        the aliquots; and    -   d) selecting one of the test compositions which significantly        reduces the level of expression of the marker in the aliquot        containing that test composition, relative to the levels of        expression of the marker in the presence of the other test        compositions.

The invention additionally provides a test method of assessing thebreast carcinogenic potential of a compound. This method comprises thesteps of:

-   -   a) maintaining separate aliquots of breast cells in the presence        and absence of the compound; and    -   b) comparing expression of a marker of the invention in each of        the aliquots.        A significantly higher level of expression of the marker in the        aliquot maintained in the presence of the compound, relative to        that of the aliquot maintained in the absence of the compound,        is an indication that the compound possesses breast carcinogenic        potential.

In addition, the invention further provides a method of inhibitingbreast cancer in a patient. This method comprises the steps of:

-   -   a) obtaining a sample comprising cancer cells from the patient;    -   b) separately maintaining aliquots of the sample in the presence        of a plurality of compositions;    -   c) comparing expression of a marker of the invention in each of        the aliquots; and    -   d) administering to the patient at least one of the compositions        which significantly lowers the level of expression of the marker        in the aliquot containing that composition, relative to the        levels of expression of the marker in the presence of the other        compositions.

In the aforementioned methods, the samples or patient samples comprisecells obtained from the patient, e.g., a lump biopsy, body fluidsincluding blood fluids, lymph and cystic fluids, as well as nippleaspirates. In a further embodiment, the patient sample is in vivo.

According to the invention, the level of expression of a marker of theinvention in a sample can be assessed, for example, by detecting thepresence in the sample of:

-   -   the corresponding marker protein (e.g., a protein having one of        the sequences of SEQ ID NO (AAs)) or a fragment of the protein        (e.g. by using a reagent, such as an antibody, an antibody        derivative, an antibody fragment or single-chain antibody, which        binds specifically with the protein or protein fragment)    -   the corresponding marker nucleic acid (e.g. a nucleotide        transcript having one of the sequences of the SEQ ID NO (nts)),        or a complement thereof), or a fragment of the nucleic acid        (e.g. by contacting transcribed polynucleotides obtained from        the sample with a substrate having affixed thereto one or more        nucleic acids having the entire or a segment of the sequence of        any of the SEQ ID NO (nts)), or a complement thereof)    -   a metabolite which is produced directly (i.e., catalyzed) or        indirectly by the corresponding marker protein.

According to the invention, any of the aforementioned methods may beperformed using a plurality (e.g. 2, 3, 5, or 10 or more) of breastcancer markers, including breast cancer markers known in the art. Insuch methods, the level of expression in the sample of each of aplurality of markers, at least one of which is a marker of theinvention, is compared with the normal level of expression of each ofthe plurality of markers in samples of the same type obtained fromcontrol humans not afflicted with breast cancer. A significantly altered(i.e., increased or decreased as specified in the above-describedmethods using a single marker) level of expression in the sample of oneor more markers of the invention, or some combination thereof, relativeto that marker's corresponding normal or control level, is an indicationthat the patient is afflicted with breast cancer. For all of theaforementioned methods, the marker(s) are preferably selected such thatthe positive predictive value of the method is at least about 10%.

In a further aspect, the invention provides an antibody, an antibodyderivative, or an antibody fragment, which binds specifically with amarker protein (e.g., a protein having the sequence of any of the SEQ IDNO (AAs)) or a fragment of the protein. The invention also providesmethods for making such antibody, antibody derivative, and antibodyfragment. Such methods may comprise immunizing a mammal with a proteinor peptide comprising the entirety, or a segment of 10 or more aminoacids, of a marker protein (e.g., a protein having the sequence of anyof the SEQ ID NO (AAs)), wherein the protein or peptide may be obtainedfrom a cell or by chemical synthesis. The methods of the invention alsoencompass producing monoclonal and single-chain antibodies, which wouldfurther comprise isolating splenocytes from the immunized mammal, fusingthe isolated splenocytes with an immortalized cell line to formhybridomas, and screening individual hybridomas for those that producean antibody that binds specifically with a marker protein or a fragmentof the protein.

In another aspect, the invention relates to various diagnostic and testkits. In one embodiment, the invention provides a kit for assessingwhether a patient is afflicted with breast cancer. The kit comprises areagent for assessing expression of a marker of the invention. Inanother embodiment, the invention provides a kit for assessing thesuitability of a chemical or biologic agent for inhibiting breast cancerin a patient. Such a kit comprises a reagent for assessing expression ofa marker of the invention, and may also comprise one or more of suchagents. In a further embodiment, the invention provides kits forassessing the presence of breast cancer cells or treating breastcancers. Such kits comprise an antibody, an antibody derivative, or anantibody fragment, which binds specifically with a marker protein, or afragment of the protein. Such kits may also comprise a plurality ofantibodies, antibody derivatives, or antibody fragments wherein theplurality of such antibody agents binds specifically with a markerprotein, or a fragment of the protein.

In an additional embodiment, the invention also provides a kit forassessing the presence of breast cancer cells, wherein the kit comprisesa nucleic acid probe that binds specifically with a marker nucleic acidor a fragment of the nucleic acid. The kit may also comprise a pluralityof probes, wherein each of the probes binds specifically with a markernucleic acid, or a fragment of the nucleic acid.

In a further aspect, the invention relates to methods for treating apatient afflicted with breast cancer or at risk of developing breastcancer. Such methods may comprise reducing the expression and/orinterfering with the biological function of a marker of the invention.In one embodiment, the method comprises providing to the patient anantisense oligonucleotide or polynucleotide complementary to a markernucleic acid, or a segment thereof. For example, an antisensepolynucleotide may be provided to the patient through the delivery of avector that expresses an anti-sense polynucleotide of a marker nucleicacid or a fragment thereof. In another embodiment, the method comprisesproviding to the patient an antibody, an antibody derivative, orantibody fragment, which binds specifically with a marker protein or afragment of the protein. In a preferred embodiment, the antibody,antibody derivative or antibody fragment binds specifically with aprotein having the sequence of a SEQ ID NO (AAs), or a fragment of theprotein.

It will be appreciated that the methods and kits of the presentinvention may also include known cancer markers including known breastcancer markers. It will further be appreciated that the methods and kitsmay be used to identify cancers other than breast cancer.

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to newly discovered breast cancer markersassociated with the cancerous state of breast cells. It has beendiscovered that the higher than normal level of expression of any ofthese markers or combination of these markers correlates with thepresence of breast cancer in a patient. Methods are provided fordetecting the presence of breast cancer in a sample, the absence ofbreast cancer in a sample, the stage of breast cancer, assessing whethera breast cancer has metastasized, predicting the likely clinical outcomeof a breast cancer patient, and with other characteristics of breastcancer that are relevant to prevention, diagnosis, characterization, andtherapy of breast cancer in a patient. Methods of treating breast cancerare also provided.

Table 1 lists all of the markers of the invention, which areover-expressed in breast cancer cells compared to normal (i.e.,non-cancerous) breast cells. Table 2 lists markers identified bytranscription profiling using mRNA from 23 IDC node negative breasttumors with good outcome and 16 IDC node negative breast tumors withpoor clinical outcome. Table 3 lists markers identified by transcriptionprofiling using mRNA from 16 IDC node negative breast tumors and 19 IDCnode positive breast tumors. Table 4 lists markers identified bytranscription profiling using mRNA from 25 IDC node negative breasttumors with good outcome and 18 IDC node negative breast tumors withpoor clinical outcome. Table 5 lists markers particularly useful inscreening for the presence of breast cancer (“screening markers”). Table6 lists markers particularly useful in assessing aggressiveness ofbreast cancer (“aggressiveness markers”). Table 7 lists markersparticularly useful for both screening breast cancer and assessingaggressiveness of breast cancer. Table 8 lists markers whoseover-expression correlates with good clinical outcome, i.e., greaterthan 5 years of disease-free survival. Table 9 lists markers whoseover-expression correlates with poor clinical outcome, i.e., less than 3years of disease-free survival. Table 10 lists newly identified nucleicacid and amino acid sequences. Table 11 lists newly identified nucleicacid sequences. Table 12 lists staging markers whose expressioncorrelates with metastasis to lymph nodes.

DEFINITIONS

As used herein, each of the following terms has the meaning associatedwith it in this section.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e. to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

A “marker” is a gene whose altered level of expression in a tissue orcell from its expression level in normal or healthy tissue or cell isassociated with a disease state, such as cancer. A “marker nucleic acid”is a nucleic acid (e.g., mRNA, cDNA) encoded by or corresponding to amarker of the invention. Such marker nucleic acids include DNA (e.g.,cDNA) comprising the entire or a partial sequence of any of the SEQ IDNO (nts) or the complement of such a sequence. The marker nucleic acidsalso include RNA comprising the entire or a partial sequence of any SEQID NO (nts) or the complement of such a sequence, wherein all thymidineresidues are replaced with uridine residues. A “marker protein” is aprotein encoded by or corresponding to a marker of the invention. Amarker protein comprises the entire or a partial sequence of any of theSEQ ID NO (AAs). The terms “protein” and “polypeptide' are usedinterchangeably.

The term “probe” refers to any molecule which is capable of selectivelybinding to a specifically intended target molecule, for example, anucleotide transcript or protein encoded by or corresponding to amarker. Probes can be either synthesized by one skilled in the art, orderived from appropriate biological preparations. For purposes ofdetection of the target molecule, probes may be specifically designed tobe labeled, as described herein. Examples of molecules that can beutilized as probes include, but are not limited to, RNA, DNA, proteins,antibodies, and organic molecules.

A “breast-associated” body fluid is a fluid which, when in the body of apatient, contacts or passes through breast cells or into which cells,nucleic acids or proteins shed from breast cells are capable of passing.Exemplary breast-associated body fluids include blood fluids, lymph,cystic fluid, and nipple aspirates.

The “normal” level of expression of a marker is the level of expressionof the marker in breast cells of a human subject or patient notafflicted with breast cancer.

An “over-expression” or “significantly higher level of expression” of amarker refers to an expression level in a test sample that is greaterthan the standard error of the assay employed to assess expression, andis preferably at least twice, and more preferably three, four, five orten times the expression level of the marker in a control sample (e.g.,sample from a healthy subjects not having the marker associated disease)and preferably, the average expression level of the marker in severalcontrol samples.

A “significantly lower level of expression” of a marker refers to anexpression level in a test sample that is at least twice, and morepreferably three, four, five or ten times lower than the expressionlevel of the marker in a control sample (e.g., sample from a healthysubjects not having the marker associated disease) and preferably, theaverage expression level of the marker in several control samples.

As used herein, the term “promoter/regulatory sequence” means a nucleicacid sequence which is required for expression of a gene productoperably linked to the promoter/regulatory sequence. In some instances,this sequence may be the core promoter sequence and in other instances,this sequence may also include an enhancer sequence and other regulatoryelements which are required for expression of the gene product. Thepromoter/regulatory sequence may, for example, be one which expressesthe gene product in a tissue-specific manner.

A “constitutive” promoter is a nucleotide sequence which, when operablylinked with a polynucleotide which encodes or specifies a gene product,causes the gene product to be produced in a living human cell under mostor all physiological conditions of the cell.

An “inducible” promoter is a nucleotide sequence which, when operablylinked with a polynucleotide which encodes or specifies a gene product,causes the gene product to be produced in a living human cellsubstantially only when an inducer which corresponds to the promoter ispresent in the cell.

A “tissue-specific” promoter is a nucleotide sequence which, whenoperably linked with a polynucleotide which encodes or specifies a geneproduct, causes the gene product to be produced in a living human cellsubstantially only if the cell is a cell of the tissue typecorresponding to the promoter.

A “transcribed polynucleotide” or “nucleotide transcript” is apolynucleotide (e.g. an mRNA, hnRNA, a cDNA, or an analog of such RNA orcDNA) which is complementary to or homologous with all or a portion of amature mRNA made by transcription of a marker of the invention andnormal post-transcriptional processing (e.g. splicing), if any, of theRNA transcript, and reverse transcription of the RNA transcript.

“Complementary” refers to the broad concept of sequence complementaritybetween regions of two nucleic acid strands or between two regions ofthe same nucleic acid strand. It is known that an adenine residue of afirst nucleic acid region is capable of forming specific hydrogen bonds(“base pairing”) with a residue of a second nucleic acid region which isantiparallel to the first region if the residue is thymine or uracil.Similarly, it is known that a cytosine residue of a first nucleic acidstrand is capable of base pairing with a residue of a second nucleicacid strand which is antiparallel to the first strand if the residue isguanine. A first region of a nucleic acid is complementary to a secondregion of the same or a different nucleic acid if, when the two regionsare arranged in an antiparallel fashion, at least one nucleotide residueof the first region is capable of base pairing with a residue of thesecond region. Preferably, the first region comprises a first portionand the second region comprises a second portion, whereby, when thefirst and second portions are arranged in an antiparallel fashion, atleast about 50%, and preferably at least about 75%, at least about 90%,or at least about 95% of the nucleotide residues of the first portionare capable of base pairing with nucleotide residues in the secondportion. More preferably, all nucleotide residues of the first portionare capable of base pairing with nucleotide residues in the secondportion.

“Homologous” as used herein, refers to nucleotide sequence similaritybetween two regions of the same nucleic acid strand or between regionsof two different nucleic acid strands. When a nucleotide residueposition in both regions is occupied by the same nucleotide residue,then the regions are homologous at that position. A first region ishomologous to a second region if at least one nucleotide residueposition of each region is occupied by the same residue. Homologybetween two regions is expressed in terms of the proportion ofnucleotide residue positions of the two regions that are occupied by thesame nucleotide residue. By way of example, a region having thenucleotide sequence 5′-ATTGCC-3′ and a region having the nucleotidesequence 5′-TATGGC-3′ share 50% homology. Preferably, the first regioncomprises a first portion and the second region comprises a secondportion, whereby, at least about 50%, and preferably at least about 75%,at least about 90%, or at least about 95% of the nucleotide residuepositions of each of the portions are occupied by the same nucleotideresidue. More preferably, all nucleotide residue positions of each ofthe portions are occupied by the same nucleotide residue.

A molecule is “fixed” or “affixed” to a substrate if it is covalently ornon-covalently associated with the substrate such the substrate can berinsed with a fluid (e.g. standard saline citrate, pH 7.4) without asubstantial fraction of the molecule dissociating from the substrate.

As used herein, a “naturally-occurring” nucleic acid molecule refers toan RNA or DNA molecule having a nucleotide sequence that occurs in anorganism found in nature.

A cancer is “inhibited” if at least one symptom of the cancer isalleviated, terminated, slowed, or prevented. As used herein, breastcancer is also “inhibited” if recurrence or metastasis of the cancer isreduced, slowed, delayed, or prevented.

A kit is any manufacture (e.g. a package or container) comprising atleast one reagent, e.g. a probe, for specifically detecting theexpression of a marker of the invention. The kit may be promoted,distributed, or sold as a unit for performing the methods of the presentinvention.

“Proteins of the invention” encompass marker proteins and theirfragments; variant marker proteins and their fragments; peptides andpolypeptides comprising an at least 15 amino acid segment of a marker orvariant marker protein; and fusion proteins comprising a marker orvariant marker protein, or an at least 15 amino acid segment of a markeror variant marker protein.

Unless otherwise specified herewithin, the terms “antibody” and“antibodies” broadly encompass naturally-occurring forms of antibodies(e.g., IgG, IgA, IgM, IgE) and recombinant antibodies such assingle-chain antibodies, chimeric and humanized antibodies andmulti-specific antibodies, as well as fragments and derivatives of allof the foregoing, which fragments and derivatives have at least anantigenic binding site. Antibody derivatives may comprise a protein orchemical moiety conjugated to an antibody.

DESCRIPTION

The present invention is based, in part, on newly identified markerswhich are over-expressed in breast cancer cells as compared to theirexpression in normal (i.e. non-cancerous) breast cells. The enhancedexpression of one or more of these markers in breast cells is hereincorrelated with the cancerous state of the tissue. An enhancedexpression of some of these markers is also correlated with the stage,nodal status and clinical outcome of the patient. The invention providescompositions, kits, and methods for assessing the cancerous state ofbreast cells (e.g. cells obtained from a human, cultured human cells,archived or preserved human cells and in vivo cells) as well as treatingpatients afflicted with breast cancer.

The compositions, kits, and methods of the invention have the followinguses, among others:

-   -   1) assessing whether a patient is afflicted with breast cancer;    -   2) assessing the stage of breast cancer in a human patient;    -   3) predicting the clinical outcome of a breast cancer patient;    -   4) assessing the grade of breast cancer in a patient;    -   5) assessing the benign or malignant nature of breast cancer in        a patient;    -   6) assessing the metastatic potential of breast cancer in a        patient;    -   7) determining if breast cancer has metastasized to lymph nodes;    -   8) assessing the histological type of neoplasm associated with        breast cancer in a patient;    -   9) making antibodies, antibody fragments or antibody derivatives        that are useful for treating breast cancer and/or assessing        whether a patient is afflicted with breast cancer;    -   10) assessing the presence of breast cancer cells;    -   11) assessing the efficacy of one or more test compounds for        inhibiting breast cancer in a patient;    -   12) assessing the efficacy of a therapy for inhibiting breast        cancer in a patient;    -   13) monitoring the progression of breast cancer in a patient;    -   14) selecting a composition or therapy for inhibiting breast        cancer in a patient;    -   15) treating a patient afflicted with breast cancer;    -   16) inhibiting breast cancer in a patient;    -   17) assessing the breast carcinogenic potential of a test        compound; and    -   18) preventing the onset of breast cancer in a patient at risk        for developing breast cancer.

The invention thus includes a method of assessing whether a patient isafflicted with breast cancer. This method comprises comparing the levelof expression of a marker of the invention (listed in Table 1) in apatient sample and the normal level of expression of the marker in acontrol, e.g., a non-breast cancer sample. A significantly higher levelof expression of the marker in the patient sample as compared to thenormal level is an indication that the patient is afflicted with breastcancer.

Gene delivery vehicles, host cells and compositions (all describedherein) containing nucleic acids comprising the entirety, or a segmentof 15 or more nucleotides, of any of the sequences of SEQ ID NO (nts) orthe complement of such sequences, and polypeptides comprising theentirety, or a segment of 10 or more amino acids, of any of thesequences of SEQ ID NO (AAs) are also provided by this invention.

As described herein, breast cancer in patients is associated with anincreased level of expression of one or more markers of the invention.While, as discussed above, some of these changes in expression levelresult from occurrence of the breast cancer, others of these changesinduce, maintain, and promote the cancerous state of breast cancercells. Thus, breast cancer characterized by an increase in the level ofexpression of one or more markers of the invention can be inhibited byreducing and/or interfering with the expression of the markers and/orfunction of the proteins encoded by those markers.

Expression of a marker of the invention can be inhibited in a number ofways generally known in the art. For example, an antisenseoligonucleotide can be provided to the breast cancer cells in order toinhibit transcription, translation, or both, of the marker(s).Alternately, a polynucleotide encoding an antibody, an antibodyderivative, or an antibody fragment which specifically binds a markerprotein, and operably linked with an appropriate promoter/regulatorregion, can be provided to the cell in order to generate intracellularantibodies which will inhibit the function or activity of the protein.The expression and/or function of a marker may also be inhibited bytreating the breast cancer cell with an antibody, antibody derivative orantibody fragment that specifically binds a marker protein. Using themethods described herein, a variety of molecules, particularly includingmolecules sufficiently small that they are able to cross the cellmembrane, can be screened in order to identify molecules which inhibitexpression of a marker or inhibit the function of a marker protein. Thecompound so identified can be provided to the patient in order toinhibit breast cancer cells of the patient.

Any marker or combination of markers of the invention, as well as anyknown markers in combination with the markers of the invention, may beused in the compositions, kits, and methods of the present invention. Ingeneral, it is preferable to use markers for which the differencebetween the level of expression of the marker in breast cancer cells andthe level of expression of the same marker in normal breast cells is asgreat as possible. Although this difference can be as small as the limitof detection of the method for assessing expression of the marker, it ispreferred that the difference be at least greater than the standarderror of the assessment method, and preferably a difference of at least2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 25-, 100-, 500-,1000-fold or greater than the level of expression of the same marker innormal breast tissue.

It is recognized that certain marker proteins are secreted from breastcells (i.e. one or both of normal and cancerous cells) to theextracellular space surrounding the cells. These markers are preferablyused in certain embodiments of the compositions, kits, and methods ofthe invention, owing to the fact that the such marker proteins can bedetected in a breast-associated body fluid sample, which may be moreeasily collected from a human patient than a tissue biopsy sample. Inaddition, preferred in vivo techniques for detection of a marker proteininclude introducing into a subject a labeled antibody directed againstthe protein. For example, the antibody can be labeled with a radioactivemarker whose presence and location in a subject can be detected bystandard imaging techniques.

It is a simple matter for the skilled artisan to determine whether anyparticular marker protein is a secreted protein. In order to make thisdetermination, the marker protein is expressed in, for example, amammalian cell, preferably a human breast cell line, extracellular fluidis collected, and the presence or absence of the protein in theextracellular fluid is assessed (e.g. using a labeled antibody whichbinds specifically with the protein).

The following is an example of a method which can be used to detectsecretion of a protein. About 8×10⁵ 293T cells are incubated at 37° c.in wells containing growth medium (Dulbecco's modified Eagle's medium{DMEM} supplemented with 10% fetal bovine serum) under a 5% (v/v) CO₂,95% air atmosphere to about 60-70% confluence. The cells are thentransfected using a standard transfection mixture comprising 2micrograms of DNA comprising an expression vector encoding the proteinand 10 microliters of LipofectAMINE™ (GIBCO/BRL Catalog no. 18342-012)per well. The transfection mixture is maintained for about 5 hours, andthen replaced with fresh growth medium and maintained in an airatmosphere. Each well is gently rinsed twice with DMEM which does notcontain methionine or cysteine (DMEM-MC; ICN Catalog no. 16-424-54).About 1 milliliter of DMEM-MC and about 50 microcuries of Trans-³⁵S™reagent (ICN Catalog no. 51006) are added to each well. The wells aremaintained under the 5% CO₂ atmosphere described above and incubated at37° C. for a selected period. Following incubation, 150 microliters ofconditioned medium is removed and centrifuged to remove floating cellsand debris. The presence of the protein in the supernatant is anindication that the protein is secreted.

It will be appreciated that patient samples containing breast cells maybe used in the methods of the present invention. In these embodiments,the level of expression of the marker can be assessed by assessing theamount (e.g. absolute amount or concentration) of the marker in a breastcell sample, e.g., breast biopsies obtained from a patient. The cellsample can, of course, be subjected to a variety of well-knownpost-collection preparative and storage techniques (e.g., nucleic acidand/or protein extraction, fixation, storage, freezing, ultrafiltration,concentration, evaporation, centrifugation, etc.) prior to assessing theamount of the marker in the sample. Likewise, breast biopsies may alsobe subjected to post-collection preparative and storage techniques,e.g., fixation.

The compositions, kits, and methods of the invention can be used todetect expression of marker proteins having at least one portion whichis displayed on the surface of cells which express it. It is a simplematter for the skilled artisan to determine whether a marker protein, ora portion thereof, is exposed on the cell surface. For example,immunological methods may be used to detect such proteins on wholecells, or well known computer-based sequence analysis methods may beused to predict the presence of at least one extracellular domain (i.e.including both secreted proteins and proteins having at least onecell-surface domain). Expression of a marker protein having at least oneportion which is displayed on the surface of a cell which expresses itmay be detected without necessarily lysing the cell (e.g. using alabeled antibody which binds specifically with a cell-surface domain ofthe protein).

Expression of a marker of the invention may be assessed by any of a widevariety of well known methods for detecting expression of a transcribednucleic acid or protein. Non-limiting examples of such methods includeimmunological methods for detection of secreted, cell-surface,cytoplasmic, or nuclear proteins, protein purification methods, proteinfunction or activity assays, nucleic acid hybridization methods, nucleicacid reverse transcription methods, and nucleic acid amplificationmethods.

In a preferred embodiment, expression of a marker is assessed using anantibody (e.g. a radio-labeled, chromophore-labeled,fluorophore-labeled, or enzyme-labeled antibody), an antibody derivative(e.g. an antibody conjugated with a substrate or with the protein orligand of a protein-ligand pair {e.g. biotin-streptavidin}), or anantibody fragment (e.g. a single-chain antibody, an isolated antibodyhypervariable domain, etc.) which binds specifically with a markerprotein or fragment thereof, including a marker protein which hasundergone all or a portion of its normal post-translationalmodification.

In another preferred embodiment, expression of a marker is assessed bypreparing mRNA/cDNA (i.e. a transcribed polynucleotide) from cells in apatient sample, and by hybridizing the mRNA/cDNA with a referencepolynucleotide which is a complement of a marker nucleic acid, or afragment thereof. cDNA can, optionally, be amplified using any of avariety of polymerase chain reaction methods prior to hybridization withthe reference polynucleotide; preferably, it is not amplified.Expression of one or more markers can likewise be detected usingquantitative PCR to assess the level of expression of the marker(s).Alternatively, any of the many known methods of detecting mutations orvariants (e.g. single nucleotide polymorphisms, deletions, etc.) of amarker of the invention may be used to detect occurrence of a marker ina patient.

In a related embodiment, a mixture of transcribed polynucleotidesobtained from the sample is contacted with a substrate having fixedthereto a polynucleotide complementary to or homologous with at least aportion (e.g. at least 7, 10, 15, 20, 25, 30, 40, 50, 100, 500, or morenucleotide residues) of a marker nucleic acid. If polynucleotidescomplementary to or homologous with are differentially detectable on thesubstrate (e.g. detectable using different chromophores or fluorophores,or fixed to different selected positions), then the levels of expressionof a plurality of markers can be assessed simultaneously using a singlesubstrate (e.g. a “gene chip” microarray of polynucleotides fixed atselected positions). When a method of assessing marker expression isused which involves hybridization of one nucleic acid with another, itis preferred that the hybridization be performed under stringenthybridization conditions.

Because the compositions, kits, and methods of the invention rely ondetection of a difference in expression levels of one or more markers ofthe invention, it is preferable that the level of expression of themarker is significantly greater than the minimum detection limit of themethod used to assess expression in at least one of normal breast cellsand cancerous breast cells.

It is understood that by routine screening of additional patient samplesusing one or more of the markers of the invention, it will be realizedthat certain of the markers are over-expressed in cancers of varioustypes, including specific breast cancers, as well as other cancers suchas lung cancer, ovarian cancer, etc. For example, it will be confirmedthat some of the markers of the invention are over-expressed in most(i.e. 50% or more) or substantially all (i.e. 80% or more) of breastcancer. Furthermore, it will be confirmed that certain of the markers ofthe invention are associated with breast cancer of various stages (i.e.stage 0, I, II, II, and IV breast cancers, as well as subclassificationsIIA, IIB, IIIA, and IIIB, using the FIGO Stage Grouping system forprimary carcinoma of the breast; (see Breast, In: American JointCommittee on Cancer: AJCC Cancer Staging Manual. Lippincott-RavenPublishers, 5th ed., 1997, pp. 171-180), of various histologic subtypes(e.g. serous, mucinous, endometroid, and clear cell subtypes, as well assubclassifications and alternate classifications adenocarcinoma,papillary adenocarcinoma, papillary cystadenocarcinoma, surfacepapillary carcinoma, malignant adenofibroma, cystadenofibroma,adenocarcinoma, cystadenocarcinoma, adenoacanthoma, endometrioid stromalsarcoma, mesodermal (Müllerian) mixed tumor, mesonephroid tumor,malignant carcinoma, Brenner tumor, mixed epithelial tumor, andundifferentiated carcinoma, using the WHO/FIGO system for classificationof malignant breast tumors; Scully, Atlas of Tumor Pathology, 3d series,Washington D.C.), and various grades (i.e. grade I {welldifferentiated}, grade II {moderately well differentiated}, and gradeIII {poorly differentiated from surrounding normal tissue})). Inaddition, as a greater number of patient samples are assessed forexpression of the markers of the invention and the outcomes of theindividual patients from whom the samples were obtained are correlated,it will also be confirmed that altered expression of certain of themarkers of the invention are strongly correlated with malignant cancersand that altered expression of other markers of the invention arestrongly correlated with benign tumors. The compositions, kits, andmethods of the invention are thus useful for characterizing one or moreof the stage, grade, histological type, and benign/malignant nature ofbreast cancer in patients.

When the compositions, kits, and methods of the invention are used forcharacterizing one or more of the stage, grade, histological type, andbenign/malignant nature of breast cancer in a patient, it is preferredthat the marker or panel of markers of the invention is selected suchthat a positive result is obtained in at least about 20%, and preferablyat least about 40%, 60%, or 80%, and more preferably in substantiallyall patients afflicted with a breast cancer of the corresponding stage,grade, histological type, or benign/malignant nature. Preferably, themarker or panel of markers of the invention is selected such that apositive predictive value (PPV) of greater than about 10% is obtainedfor the general population (more preferably coupled with an assayspecificity greater than 80%).

When a plurality of markers of the invention are used in thecompositions, kits, and methods of the invention, the level ofexpression of each marker in a patient sample can be compared with thenormal level of expression of each of the plurality of markers innon-cancerous samples of the same type, either in a single reactionmixture (i.e. using reagents, such as different fluorescent probes, foreach marker) or in individual reaction mixtures corresponding to one ormore of the markers. In one embodiment, a significantly increased levelof expression of more than one of the plurality of markers in thesample, relative to the corresponding normal levels, is an indicationthat the patient is afflicted with breast cancer. When a plurality ofmarkers is used, it is preferred that 2, 3, 4, 5, 8, 10, 12, 15, 20, 30,or 50 or more individual markers be used, wherein fewer markers arepreferred.

In order to maximize the sensitivity of the compositions, kits, andmethods of the invention (i.e. by interference attributable to cells ofnon-breast origin in a patient sample), it is preferable that the markerof the invention used therein be a marker which has a restricted tissuedistribution, e.g., normally not expressed in a non-breast tissue.

Only a small number of markers are known to be associated with breastcancers (e.g. BRCA1 and BRCA2). These markers are not, of course,included among the markers of the invention, although they may be usedtogether with one or more markers of the invention in a panel ofmarkers, for example. It is well known that certain types of genes, suchas oncogenes, tumor suppressor genes, growth factor-like genes,protease-like genes, and protein kinase-like genes are often involvedwith development of cancers of various types. Thus, among the markers ofthe invention, use of those which correspond to proteins which resembleknown proteins encoded by known oncogenes and tumor suppressor genes,and those which correspond to proteins which resemble growth factors,proteases, and protein kinases are preferred.

It is recognized that the compositions, kits, and methods of theinvention will be of particular utility to patients having an enhancedrisk of developing breast cancer and their medical advisors. Patientsrecognized as having an enhanced risk of developing breast cancerinclude, for example, patients having a familial history of breastcancer, patients identified as having a mutant oncogene (i.e. at leastone allele), and patients of advancing age (i.e. women older than about50 or 60 years).

The level of expression of a marker in normal (i.e. non-cancerous)breast tissue can be assessed in a variety of ways. In one embodiment,this normal level of expression is assessed by assessing the level ofexpression of the marker in a portion of breast cells which appears tobe non-cancerous and by comparing this normal level of expression withthe level of expression in a portion of the breast cells which issuspected of being cancerous. Alternately, and particularly as furtherinformation becomes available as a result of routine performance of themethods described herein, population-average values for normalexpression of the markers of the invention may be used. In otherembodiments, the ‘normal’ level of expression of a marker may bedetermined by assessing expression of the marker in a patient sampleobtained from a non-cancer-afflicted patient, from a patient sampleobtained from a patient before the suspected onset of breast cancer inthe patient, from archived patient samples, and the like.

The invention includes compositions, kits, and methods for assessing thepresence of breast cancer cells in a sample (e.g. an archived tissuesample or a sample obtained from a patient). These compositions, kits,and methods are substantially the same as those described above, exceptthat, where necessary, the compositions, kits, and methods are adaptedfor use with samples other than patient samples. For example, when thesample to be used is a parafinized, archived human tissue sample, it canbe necessary to adjust the ratio of compounds in the compositions of theinvention, in the kits of the invention, or the methods used to assesslevels of marker expression in the sample. Such methods are well knownin the art and within the skill of the ordinary artisan.

The invention includes a kit for assessing the presence of breast cancercells (e.g. in a sample such as a patient sample). The kit comprises aplurality of reagents, each of which is capable of binding specificallywith a marker nucleic acid or protein. Suitable reagents for bindingwith a marker protein include antibodies, antibody derivatives, antibodyfragments, and the like. Suitable reagents for binding with a markernucleic acid (e.g. a genomic DNA, an mRNA, a spliced mRNA, a cDNA, orthe like) include complementary nucleic acids. For example, the nucleicacid reagents may include oligonucleotides (labeled or non-labeled)fixed to a substrate, labeled oligonucleotides not bound with asubstrate, pairs of PCR primers, molecular beacon probes, and the like.

The kit of the invention may optionally comprise additional componentsuseful for performing the methods of the invention. By way of example,the kit may comprise fluids (e.g. SSC buffer) suitable for annealingcomplementary nucleic acids or for binding an antibody with a proteinwith which it specifically binds, one or more sample compartments, aninstructional material which describes performance of a method of theinvention, a sample of normal breast cells, a sample of breast cancercells, and the like.

The invention also includes a method of making an isolated hybridomawhich produces an antibody useful for assessing whether a patient isafflicted with breast cancer. In this method, a protein or peptidecomprising the entirety or a segment of a marker protein is synthesizedor isolated (e.g. by purification from a cell in which it is expressedor by transcription and translation of a nucleic acid encoding theprotein or peptide in vivo or in vitro using known methods). Avertebrate, preferably a mammal such as a mouse, rat, rabbit, or sheep,is immunized using the protein or peptide. The vertebrate may optionally(and preferably) be immunized at least one additional time with theprotein or peptide, so that the vertebrate exhibits a robust immuneresponse to the protein or peptide. Splenocytes are isolated from theimmunized vertebrate and fused with an immortalized cell line to formhybridomas, using any of a variety of methods well known in the art.Hybridomas formed in this manner are then screened using standardmethods to identify one or more hybridomas which produce an antibodywhich specifically binds with the marker protein or a fragment thereof.The invention also includes hybridomas made by this method andantibodies made using such hybridomas.

The invention also includes a method of assessing the efficacy of a testcompound for inhibiting breast cancer cells. As described above,differences in the level of expression of the markers of the inventioncorrelate with the cancerous state of breast cells. Although it isrecognized that changes in the levels of expression of certain of themarkers of the invention likely result from the cancerous state ofbreast cells, it is likewise recognized that changes in the levels ofexpression of other of the markers of the invention induce, maintain,and promote the cancerous state of those cells. Thus, compounds whichinhibit a breast cancer in a patient will cause the level of expressionof one or more of the markers of the invention to change to a levelnearer the normal level of expression for that marker (i.e. the level ofexpression for the marker in non-cancerous breast cells).

This method thus comprises comparing expression of a marker in a firstbreast cell sample and maintained in the presence of the test compoundand expression of the marker in a second breast cell sample andmaintained in the absence of the test compound. A significantly reducedexpression of a marker of the invention in the presence of the testcompound is an indication that the test compound inhibits breast cancer.The breast cell samples may, for example, be aliquots of a single sampleof normal breast cells obtained from a patient, pooled samples of normalbreast cells obtained from a patient, cells of a normal breast cellline, aliquots of a single sample of breast cancer cells obtained from apatient, pooled samples of breast cancer cells obtained from a patient,cells of a breast cancer cell line, or the like. In one embodiment, thesamples are breast cancer cells obtained from a patient and a pluralityof compounds known to be effective for inhibiting various breast cancersare tested in order to identify the compound which is likely to bestinhibit the breast cancer in the patient.

This method may likewise be used to assess the efficacy of a therapy forinhibiting breast cancer in a patient. In this method, the level ofexpression of one or more markers of the invention in a pair of samples(one subjected to the therapy, the other not subjected to the therapy)is assessed. As with the method of assessing the efficacy of testcompounds, if the therapy induces a significantly lower level ofexpression of a marker of the invention then the therapy is efficaciousfor inhibiting breast cancer. As above, if samples from a selectedpatient are used in this method, then alternative therapies can beassessed in vitro in order to select a therapy most likely to beefficacious for inhibiting breast cancer in the patient.

As described above, the cancerous state of human breast cells iscorrelated with changes in the levels of expression of the markers ofthe invention. The invention includes a method for assessing the humanbreast cell carcinogenic potential of a test compound. This methodcomprises maintaining separate aliquots of human breast cells in thepresence and absence of the test compound. Expression of a marker of theinvention in each of the aliquots is compared. A significantly higherlevel of expression of a marker of the invention in the aliquotmaintained in the presence of the test compound (relative to the aliquotmaintained in the absence of the test compound) is an indication thatthe test compound possesses human breast cell carcinogenic potential.The relative carcinogenic potentials of various test compounds can beassessed by comparing the degree of enhancement or inhibition of thelevel of expression of the relevant markers, by comparing the number ofmarkers for which the level of expression is enhanced or inhibited, orby comparing both.

Various aspects of the invention are described in further detail in thefollowing subsections.

I. Isolated Nucleic Acid Molecules

One aspect of the invention pertains to isolated nucleic acid molecules,including nucleic acids which encode a marker protein or a portionthereof. Isolated nucleic acids of the invention also include nucleicacid molecules sufficient for use as hybridization probes to identifymarker nucleic acid molecules, and fragments of marker nucleic acidmolecules, e.g., those suitable for use as PCR primers for theamplification or mutation of marker nucleic acid molecules. As usedherein, the term “nucleic acid molecule” is intended to include DNAmolecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) andanalogs of the DNA or RNA generated using nucleotide analogs. Thenucleic acid molecule can be single-stranded or double-stranded, butpreferably is double-stranded DNA.

An “isolated” nucleic acid molecule is one which is separated from othernucleic acid molecules which are present in the natural source of thenucleic acid molecule. Preferably, an “isolated” nucleic acid moleculeis free of sequences (preferably protein-encoding sequences) whichnaturally flank the nucleic acid (i.e., sequences located at the 5′ and3′ ends of the nucleic acid) in the genomic DNA of the organism fromwhich the nucleic acid is derived. For example, in various embodiments,the isolated nucleic acid molecule can contain less than about 5 kB, 4kB, 3 kB, 2 kB, 1 kB, 0.5 kB or 0.1 kB of nucleotide sequences whichnaturally flank the nucleic acid molecule in genomic DNA of the cellfrom which the nucleic acid is derived. Moreover, an “isolated” nucleicacid molecule, such as a cDNA molecule, can be substantially free ofother cellular material, or culture medium when produced by recombinanttechniques, or substantially free of chemical precursors or otherchemicals when chemically synthesized.

A nucleic acid molecule of the present invention can be isolated usingstandard molecular biology techniques and the sequence information inthe database records described herein. Using all or a portion of suchnucleic acid sequences, nucleic acid molecules of the invention can beisolated using standard hybridization and cloning techniques (e.g., asdescribed in Sambrook et al., ed., Molecular Cloning: A LaboratoryManual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., 1989).

A nucleic acid molecule of the invention can be amplified using cDNA,mRNA, or genomic DNA as a template and appropriate oligonucleotideprimers according to standard PCR amplification techniques. The nucleicacid so amplified can be cloned into an appropriate vector andcharacterized by DNA sequence analysis. Furthermore, nucleotidescorresponding to all or a portion of a nucleic acid molecule of theinvention can be prepared by standard synthetic techniques, e.g., usingan automated DNA synthesizer.

In another preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises a nucleic acid molecule which has a nucleotidesequence complementary to the nucleotide sequence of a marker nucleicacid or to the nucleotide sequence of a nucleic acid encoding a markerprotein. A nucleic acid molecule which is complementary to a givennucleotide sequence is one which is sufficiently complementary to thegiven nucleotide sequence that it can hybridize to the given nucleotidesequence thereby forming a stable duplex.

Moreover, a nucleic acid molecule of the invention can comprise only aportion of a nucleic acid sequence, wherein the full length nucleic acidsequence comprises a marker nucleic acid or which encodes a markerprotein. Such nucleic acids can be used, for example, as a probe orprimer. The probe/primer typically is used as one or more substantiallypurified oligonucleotides. The oligonucleotide typically comprises aregion of nucleotide sequence that hybridizes under stringent conditionsto at least about 7, preferably about 15, more preferably about 25, 50,75, 100, 125, 150, 175, 200, 250, 300, 350, or 400 or more consecutivenucleotides of a nucleic acid of the invention.

Probes based on the sequence of a nucleic acid molecule of the inventioncan be used to detect transcripts or genomic sequences corresponding toone or more markers of the invention. The probe comprises a label groupattached thereto, e.g., a radioisotope, a fluorescent compound, anenzyme, or an enzyme co-factor. Such probes can be used as part of adiagnostic test kit for identifying cells or tissues which mis-expressthe protein, such as by measuring levels of a nucleic acid moleculeencoding the protein in a sample of cells from a subject, e.g.,detecting mRNA levels or determining whether a gene encoding the proteinhas been mutated or deleted.

The invention further encompasses nucleic acid molecules that differ,due to degeneracy of the genetic code, from the nucleotide sequence ofnucleic acids encoding a marker protein (e.g., protein having thesequence of a SEQ ID NO (AAs)), and thus encode the same protein.

It will be appreciated by those skilled in the art that DNA sequencepolymorphisms that lead to changes in the amino acid sequence can existwithin a population (e.g., the human population). Such geneticpolymorphisms can exist among individuals within a population due tonatural allelic variation. An allele is one of a group of genes whichoccur alternatively at a given genetic locus. In addition, it will beappreciated that DNA polymorphisms that affect RNA expression levels canalso exist that may affect the overall expression level of that gene(e.g., by affecting regulation or degradation).

As used herein, the phrase “allelic variant” refers to a nucleotidesequence which occurs at a given locus or to a polypeptide encoded bythe nucleotide sequence.

As used herein, the terms “gene” and “recombinant gene” refer to nucleicacid molecules comprising an open reading frame encoding a polypeptidecorresponding to a marker of the invention. Such natural allelicvariations can typically result in 1-5% variance in the nucleotidesequence of a given gene. Alternative alleles can be identified bysequencing the gene of interest in a number of different individuals.This can be readily carried out by using hybridization probes toidentify the same genetic locus in a variety of individuals. Any and allsuch nucleotide variations and resulting amino acid polymorphisms orvariations that are the result of natural allelic variation and that donot alter the functional activity are intended to be within the scope ofthe invention.

In another embodiment, an isolated nucleic acid molecule of theinvention is at least 7, 15, 20, 25, 30, 40, 60, 80, 100, 150, 200, 250,300, 350, 400, 450, 550, 650, 700, 800, 900, 1000, 1200, 1400, 1600,1800, 2000, 2200, 2400, 2600, 2800, 3000, 3500, 4000, 4500, or morenucleotides in length and hybridizes under stringent conditions to amarker nucleic acid or to a nucleic acid encoding a marker protein. Asused herein, the term “hybridizes under stringent conditions” isintended to describe conditions for hybridization and washing underwhich nucleotide sequences at least 60% (65%, 70%, preferably 75%)identical to each other typically remain hybridized to each other. Suchstringent conditions are known to those skilled in the art and can befound in sections 6.3.1-6.3.6 of Current Protocols in Molecular Biology,John Wiley & Sons, N.Y. (1989). A preferred, non-limiting example ofstringent hybridization conditions are hybridization in 6× sodiumchloride/sodium citrate (SSC) at about 45° C., followed by one or morewashes in 0.2×SSC, 0.1% SDS at 50-65° C.

In addition to naturally-occurring allelic variants of a nucleic acidmolecule of the invention that can exist in the population, the skilledartisan will further appreciate that sequence changes can be introducedby mutation thereby leading to changes in the amino acid sequence of theencoded protein, without altering the biological activity of the proteinencoded thereby. For example, one can make nucleotide substitutionsleading to amino acid substitutions at “non-essential” amino acidresidues. A “non-essential” amino acid residue is a residue that can bealtered from the wild-type sequence without altering the biologicalactivity, whereas an “essential” amino acid residue is required forbiological activity. For example, amino acid residues that are notconserved or only semi-conserved among homologs of various species maybe non-essential for activity and thus would be likely targets foralteration. Alternatively, amino acid residues that are conserved amongthe homologs of various species (e.g., murine and human) may beessential for activity and thus would not be likely targets foralteration.

Accordingly, another aspect of the invention pertains to nucleic acidmolecules encoding a variant marker protein that contain changes inamino acid residues that are not essential for activity. Such variantmarker proteins differ in amino acid sequence from thenaturally-occurring marker proteins, yet retain biological activity. Inone embodiment, such a variant marker protein has an amino acid sequencethat is at least about 40% identical, 50%, 60%, 70%, 80%, 90%, 95%, or98% identical to the amino acid sequence of a marker protein.

An isolated nucleic acid molecule encoding a variant marker protein canbe created by introducing one or more nucleotide substitutions,additions or deletions into the nucleotide sequence of marker nucleicacids, such that one or more amino acid residue substitutions,additions, or deletions are introduced into the encoded protein.Mutations can be introduced by standard techniques, such assite-directed mutagenesis and PCR-mediated mutagenesis. Preferably,conservative amino acid substitutions are made at one or more predictednon-essential amino acid residues. A “conservative amino acidsubstitution” is one in which the amino acid residue is replaced with anamino acid residue having a similar side chain. Families of amino acidresidues having similar side chains have been defined in the art. Thesefamilies include amino acids with basic side chains (e.g., lysine,arginine, histidine), acidic side chains (e.g., aspartic acid, glutamicacid), uncharged polar side chains (e.g., glycine, asparagine,glutamine, serine, threonine, tyrosine, cysteine), non-polar side chains(e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine,methionine, tryptophan), beta-branched side chains (e.g., threonine,valine, isoleucine) and aromatic side chains (e.g., tyrosine,phenylalanine, tryptophan, histidine). Alternatively, mutations can beintroduced randomly along all or part of the coding sequence, such as bysaturation mutagenesis, and the resultant mutants can be screened forbiological activity to identify mutants that retain activity. Followingmutagenesis, the encoded protein can be expressed recombinantly and theactivity of the protein can be determined.

The present invention encompasses antisense nucleic acid molecules,i.e., molecules which are complementary to a sense nucleic acid of theinvention, e.g., complementary to the coding strand of a double-strandedmarker cDNA molecule or complementary to a marker mRNA sequence.Accordingly, an antisense nucleic acid of the invention can hydrogenbond to (i.e. anneal with) a sense nucleic acid of the invention. Theantisense nucleic acid can be complementary to an entire coding strand,or to only a portion thereof, e.g., all or part of the protein codingregion (or open reading frame). An antisense nucleic acid molecule canalso be antisense to all or part of a non-coding region of the codingstrand of a nucleotide sequence encoding a marker protein. Thenon-coding regions (“5′ and 3′ untranslated regions”) are the 5′ and 3′sequences which flank the coding region and are not translated intoamino acids.

An antisense oligonucleotide can be, for example, about 5, 10, 15, 20,25, 30, 35, 40, 45, or 50 or more nucleotides in length. An antisensenucleic acid of the invention can be constructed using chemicalsynthesis and enzymatic ligation reactions using procedures known in theart. For example, an antisense nucleic acid (e.g., an antisenseoligonucleotide) can be chemically synthesized using naturally occurringnucleotides or variously modified nucleotides designed to increase thebiological stability of the molecules or to increase the physicalstability of the duplex formed between the antisense and sense nucleicacids, e.g., phosphorothioate derivatives and acridine substitutednucleotides can be used. Examples of modified nucleotides which can beused to generate the antisense nucleic acid include 5-fluorouracil,5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine,4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil,5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v),wybutoxosine, pseudouracil, queosine, 2-thiocytosine,5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v),5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, (acp3)w,and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can beproduced biologically using an expression vector into which a nucleicacid has been sub-cloned in an antisense orientation (i.e., RNAtranscribed from the inserted nucleic acid will be of an antisenseorientation to a target nucleic acid of interest, described further inthe following subsection).

The antisense nucleic acid molecules of the invention are typicallyadministered to a subject or generated in situ such that they hybridizewith or bind to cellular mRNA and/or genomic DNA encoding a markerprotein to thereby inhibit expression of the marker, e.g., by inhibitingtranscription and/or translation. The hybridization can be byconventional nucleotide complementarity to form a stable duplex, or, forexample, in the case of an antisense nucleic acid molecule which bindsto DNA duplexes, through specific interactions in the major groove ofthe double helix. Examples of a route of administration of antisensenucleic acid molecules of the invention includes direct injection at atissue site or infusion of the antisense nucleic acid into abreast-associated body fluid. Alternatively, antisense nucleic acidmolecules can be modified to target selected cells and then administeredsystemically. For example, for systemic administration, antisensemolecules can be modified such that they specifically bind to receptorsor antigens expressed on a selected cell surface, e.g., by linking theantisense nucleic acid molecules to peptides or antibodies which bind tocell surface receptors or antigens. The antisense nucleic acid moleculescan also be delivered to cells using the vectors described herein. Toachieve sufficient intracellular concentrations of the antisensemolecules, vector constructs in which the antisense nucleic acidmolecule is placed under the control of a strong pol II or pol IIIpromoter are preferred.

An antisense nucleic acid molecule of the invention can be an α-anomericnucleic acid molecule. An α-anomeric nucleic acid molecule formsspecific double-stranded hybrids with complementary RNA in which,contrary to the usual α-units, the strands run parallel to each other(Gaultier et al., 1987, Nucleic Acids Res. 15:6625-6641). The antisensenucleic acid molecule can also comprise a 2′-o-methylribonucleotide(Inoue et al., 1987, Nucleic Acids Res. 15:6131-6148) or a chimericRNA-DNA analogue (Inoue et al., 1987, FEBS Lett. 215:327-330).

The invention also encompasses ribozymes. Ribozymes are catalytic RNAmolecules with ribonuclease activity which are capable of cleaving asingle-stranded nucleic acid, such as an mRNA, to which they have acomplementary region. Thus, ribozymes (e.g., hammerhead ribozymes asdescribed in Haselhoff and Gerlach, 1988, Nature 334:585-591) can beused to catalytically cleave mRNA transcripts to thereby inhibittranslation of the protein encoded by the mRNA. A ribozyme havingspecificity for a nucleic acid molecule encoding a marker protein can bedesigned based upon the nucleotide sequence of a cDNA corresponding tothe marker. For example, a derivative of a Tetrahymena L-19 IVS RNA canbe constructed in which the nucleotide sequence of the active site iscomplementary to the nucleotide sequence to be cleaved (see Cech et al.U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742).Alternatively, an mRNA encoding a polypeptide of the invention can beused to select a catalytic RNA having a specific ribonuclease activityfrom a pool of RNA molecules (see, e.g., Bartel and Szostak, 1993,Science 261:1411-1418).

The invention also encompasses nucleic acid molecules which form triplehelical structures. For example, expression of a marker of the inventioncan be inhibited by targeting nucleotide sequences complementary to theregulatory region of the gene encoding the marker nucleic acid orprotein (e.g., the promoter and/or enhancer) to form triple helicalstructures that prevent transcription of the gene in target cells. Seegenerally Helene (1991) Anticancer Drug Des. 6(6):569-84; Helene (1992)Ann. N.Y. Acad. Sci. 660:27-36; and Maher (1992) Bioassays14(12):807-15.

In various embodiments, the nucleic acid molecules of the invention canbe modified at the base moiety, sugar moiety or phosphate backbone toimprove, e.g., the stability, hybridization, or solubility of themolecule. For example, the deoxyribose phosphate backbone of the nucleicacids can be modified to generate peptide nucleic acids (see Hyrup etal., 1996, Bioorganic & Medicinal Chemistry 4(1): 5-23). As used herein,the terms “peptide nucleic acids” or “PNAs” refer to nucleic acidmimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone isreplaced by a pseudopeptide backbone and only the four naturalnucleobases are retained. The neutral backbone of PNAs has been shown toallow for specific hybridization to DNA and RNA under conditions of lowionic strength. The synthesis of PNA oligomers can be performed usingstandard solid phase peptide synthesis protocols as described in Hyrupet al. (1996), supra; Perry-O′Keefe et al. (1996) Proc. Natl. Acad. Sci.USA 93:14670-675.

PNAs can be used in therapeutic and diagnostic applications. Forexample, PNAs can be used as antisense or antigene agents forsequence-specific modulation of gene expression by, e.g., inducingtranscription or translation arrest or inhibiting replication. PNAs canalso be used, e.g., in the analysis of single base pair mutations in agene by, e.g., PNA directed PCR clamping; as artificial restrictionenzymes when used in combination with other enzymes, e.g., S1 nucleases(Hyrup (1996), supra; or as probes or primers for DNA sequence andhybridization (Hyrup, 1996, supra; Perry-O′Keefe et al., 1996, Proc.Natl. Acad. Sci. USA 93:14670-675).

In another embodiment, PNAs can be modified, e.g., to enhance theirstability or cellular uptake, by attaching lipophilic or other helpergroups to PNA, by the formation of PNA-DNA chimeras, or by the use ofliposomes or other techniques of drug delivery known in the art. Forexample, PNA-DNA chimeras can be generated which can combine theadvantageous properties of PNA and DNA. Such chimeras allow DNArecognition enzymes, e.g., RNase H and DNA polymerases, to interact withthe DNA portion while the PNA portion would provide high bindingaffinity and specificity. PNA-DNA chimeras can be linked using linkersof appropriate lengths selected in terms of base stacking, number ofbonds between the nucleobases, and orientation (Hyrup, 1996, supra). Thesynthesis of PNA-DNA chimeras can be performed as described in Hyrup(1996), supra, and Finn et al. (1996) Nucleic Acids Res. 24(17):3357-63.For example, a DNA chain can be synthesized on a solid support usingstandard phosphoramidite coupling chemistry and modified nucleosideanalogs. Compounds such as 5′-(4-methoxytrityl)amino-5′-deoxy-thymidinephosphoramidite can be used as a link between the PNA and the 5′ end ofDNA (Mag et al., 1989, Nucleic Acids Res. 17:5973-88). PNA monomers arethen coupled in a step-wise manner to produce a chimeric molecule with a5′ PNA segment and a 3′ DNA segment (Finn et al., 1996, Nucleic AcidsRes. 24(17):3357-63). Alternatively, chimeric molecules can besynthesized with a 5′ DNA segment and a 3′ PNA segment (Peterser et al.,1975, Bioorganic Med. Chem. Lett. 5:1119-11124).

In other embodiments, the oligonucleotide can include other appendedgroups such as peptides (e.g., for targeting host cell receptors invivo), or agents facilitating transport across the cell membrane (see,e.g., Letsinger et al., 1989, Proc. Natl. Acad. Sci. USA 86:6553-6556;Lemaitre et al., 1987, Proc. Natl. Acad. Sci. USA 84:648-652; PCTPublication No. WO 88/09810) or the blood-brain bather (see, e.g., PCTPublication No. WO 89/10134). In addition, oligonucleotides can bemodified with hybridization-triggered cleavage agents (see, e.g., Krolet al., 1988, Bio/Techniques 6:958-976) or intercalating agents (see,e.g., Zon, 1988, Pharm. Res. 5:539-549). To this end, theoligonucleotide can be conjugated to another molecule, e.g., a peptide,hybridization triggered cross-linking agent, transport agent,hybridization-triggered cleavage agent, etc.

The invention also includes molecular beacon nucleic acids having atleast one region which is complementary to a nucleic acid of theinvention, such that the molecular beacon is useful for quantitating thepresence of the nucleic acid of the invention in a sample. A “molecularbeacon” nucleic acid is a nucleic acid comprising a pair ofcomplementary regions and having a fluorophore and a fluorescentquencher associated therewith. The fluorophore and quencher areassociated with different portions of the nucleic acid in such anorientation that when the complementary regions are annealed with oneanother, fluorescence of the fluorophore is quenched by the quencher.When the complementary regions of the nucleic acid are not annealed withone another, fluorescence of the fluorophore is quenched to a lesserdegree. Molecular beacon nucleic acids are described, for example, inU.S. Pat. No. 5,876,930.

II. Isolated Proteins and Antibodies

One aspect of the invention pertains to isolated marker proteins andbiologically active portions thereof, as well as polypeptide fragmentssuitable for use as immunogens to raise antibodies directed against amarker protein or a fragment thereof. In one embodiment, the nativemarker protein can be isolated from cells or tissue sources by anappropriate purification scheme using standard protein purificationtechniques. In another embodiment, a protein or peptide comprising thewhole or a segment of the marker protein is produced by recombinant DNAtechniques. Alternative to recombinant expression, such protein orpeptide can be synthesized chemically using standard peptide synthesistechniques.

An “isolated” or “purified” protein or biologically active portionthereof is substantially free of cellular material or othercontaminating proteins from the cell or tissue source from which theprotein is derived, or substantially free of chemical precursors orother chemicals when chemically synthesized. The language “substantiallyfree of cellular material” includes preparations of protein in which theprotein is separated from cellular components of the cells from which itis isolated or recombinantly produced. Thus, protein that issubstantially free of cellular material includes preparations of proteinhaving less than about 30%, 20%, 10%, or 5% (by dry weight) ofheterologous protein (also referred to herein as a “contaminatingprotein”). When the protein or biologically active portion thereof isrecombinantly produced, it is also preferably substantially free ofculture medium, i.e., culture medium represents less than about 20%,10%, or 5% of the volume of the protein preparation. When the protein isproduced by chemical synthesis, it is preferably substantially free ofchemical precursors or other chemicals, i.e., it is separated fromchemical precursors or other chemicals which are involved in thesynthesis of the protein. Accordingly such preparations of the proteinhave less than about 30%, 20%, 10%, 5% (by dry weight) of chemicalprecursors or compounds other than the polypeptide of interest.

Biologically active portions of a marker protein include polypeptidescomprising amino acid sequences sufficiently identical to or derivedfrom the amino acid sequence of the marker protein, which include feweramino acids than the full length protein, and exhibit at least oneactivity of the corresponding full-length protein. Typically,biologically active portions comprise a domain or motif with at leastone activity of the corresponding full-length protein. A biologicallyactive portion of a marker protein of the invention can be a polypeptidewhich is, for example, 10, 25, 50, 100 or more amino acids in length.Moreover, other biologically active portions, in which other regions ofthe marker protein are deleted, can be prepared by recombinanttechniques and evaluated for one or more of the functional activities ofthe native form of the marker protein.

Preferred marker proteins are encoded by nucleotide sequences comprisingthe sequence of any of the SEQ ID NO (AAs). Other useful proteins aresubstantially identical (e.g., at least about 40%, preferably 50%, 60%,70%, 80%, 90%, 95%, or 99%) to one of these sequences and retain thefunctional activity of the corresponding naturally-occurring markerprotein yet differ in amino acid sequence due to natural allelicvariation or mutagenesis.

To determine the percent identity of two amino acid sequences or of twonucleic acids, the sequences are aligned for optimal comparison purposes(e.g., gaps can be introduced in the sequence of a first amino acid ornucleic acid sequence for optimal alignment with a second amino ornucleic acid sequence). The amino acid residues or nucleotides atcorresponding amino acid positions or nucleotide positions are thencompared. When a position in the first sequence is occupied by the sameamino acid residue or nucleotide as the corresponding position in thesecond sequence, then the molecules are identical at that position. Thepercent identity between the two sequences is a function of the numberof identical positions shared by the sequences (i.e., % identity=# ofidentical positions/total # of positions (e.g., overlappingpositions)×100). In one embodiment the two sequences are the samelength.

The determination of percent identity between two sequences can beaccomplished using a mathematical algorithm. A preferred, non-limitingexample of a mathematical algorithm utilized for the comparison of twosequences is the algorithm of Karlin and Altschul (1990) Proc. Natl.Acad. Sci. USA 87:2264-2268, modified as in Karlin and Altschul (1993)Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm isincorporated into the BLASTN and BLASTX programs of Altschul, et al.(1990) J. Mol. Biol. 215:403-410. BLAST nucleotide searches can beperformed with the BLASTN program, score=100, wordlength=12 to obtainnucleotide sequences homologous to a nucleic acid molecules of theinvention. BLAST protein searches can be performed with the BLASTPprogram, score=50, wordlength=3 to obtain amino acid sequenceshomologous to a protein molecules of the invention. To obtain gappedalignments for comparison purposes, a newer version of the BLASTalgorithm called Gapped BLAST can be utilized as described in Altschulet al. (1997) Nucleic Acids Res. 25:3389-3402, which is able to performgapped local alignments for the programs BLASTN, BLASTP and BLASTX.Alternatively, PSI-Blast can be used to perform an iterated search whichdetects distant relationships between molecules. When utilizing BLAST,Gapped BLAST, and PSI-Blast programs, the default parameters of therespective programs (e.g., BLASTX and BLASTN) can be used. Seehttp://www.ncbi.nlm.nih.gov. Another preferred, non-limiting example ofa mathematical algorithm utilized for the comparison of sequences is thealgorithm of Myers and Miller, (1988) CABIOS 4:11-17. Such an algorithmis incorporated into the ALIGN program (version 2.0) which is part ofthe GCG sequence alignment software package. When utilizing the ALIGNprogram for comparing amino acid sequences, a PAM120 weight residuetable, a gap length penalty of 12, and a gap penalty of 4 can be used.Yet another useful algorithm for identifying regions of local sequencesimilarity and alignment is the FASTA algorithm as described in Pearsonand Lipman (1988) Proc. Natl. Acad. Sci. USA 85:2444-2448. When usingthe FASTA algorithm for comparing nucleotide or amino acid sequences, aPAM120 weight residue table can, for example, be used with a k-tuplevalue of 2.

The percent identity between two sequences can be determined usingtechniques similar to those described above, with or without allowinggaps. In calculating percent identity, only exact matches are counted.

The invention also provides chimeric or fusion proteins comprising amarker protein or a segment thereof. As used herein, a “chimericprotein” or “fusion protein” comprises all or part (preferably abiologically active part) of a marker protein operably linked to aheterologous polypeptide (i.e., a polypeptide other than the markerprotein). Within the fusion protein, the term “operably linked” isintended to indicate that the marker protein or segment thereof and theheterologous polypeptide are fused in-frame to each other. Theheterologous polypeptide can be fused to the amino-terminus or thecarboxyl-terminus of the marker protein or segment.

One useful fusion protein is a GST fusion protein in which a markerprotein or segment is fused to the carboxyl terminus of GST sequences.Such fusion proteins can facilitate the purification of a recombinantpolypeptide of the invention.

In another embodiment, the fusion protein contains a heterologous signalsequence at its amino terminus. For example, the native signal sequenceof a marker protein can be removed and replaced with a signal sequencefrom another protein. For example, the gp67 secretory sequence of thebaculovirus envelope protein can be used as a heterologous signalsequence (Ausubel et al., ed., Current Protocols in Molecular Biology,John Wiley & Sons, NY, 1992). Other examples of eukaryotic heterologoussignal sequences include the secretory sequences of melittin and humanplacental alkaline phosphatase (Stratagene; La Jolla, Calif.). In yetanother example, useful prokaryotic heterologous signal sequencesinclude the phoA secretory signal (Sambrook et al., supra) and theprotein A secretory signal (Pharmacia Biotech; Piscataway, N.J.).

In yet another embodiment, the fusion protein is an immunoglobulinfusion protein in which all or part of a marker protein is fused tosequences derived from a member of the immunoglobulin protein family.The immunoglobulin fusion proteins of the invention can be incorporatedinto pharmaceutical compositions and administered to a subject toinhibit an interaction between a ligand (soluble or membrane-bound) anda protein on the surface of a cell (receptor), to thereby suppresssignal transduction in vivo. The immunoglobulin fusion protein can beused to affect the bioavailability of a cognate ligand of a markerprotein Inhibition of ligand/receptor interaction can be usefultherapeutically, both for treating proliferative and differentiativedisorders and for modulating (e.g. promoting or inhibiting) cellsurvival. Moreover, the immunoglobulin fusion proteins of the inventioncan be used as immunogens to produce antibodies directed against amarker protein in a subject, to purify ligands and in screening assaysto identify molecules which inhibit the interaction of the markerprotein with ligands.

Chimeric and fusion proteins of the invention can be produced bystandard recombinant DNA techniques. In another embodiment, the fusiongene can be synthesized by conventional techniques including automatedDNA synthesizers. Alternatively, PCR amplification of gene fragments canbe carried out using anchor primers which give rise to complementaryoverhangs between two consecutive gene fragments which can subsequentlybe annealed and re-amplified to generate a chimeric gene sequence (see,e.g., Ausubel et al., supra). Moreover, many expression vectors arecommercially available that already encode a fusion moiety (e.g., a GSTpolypeptide). A nucleic acid encoding a polypeptide of the invention canbe cloned into such an expression vector such that the fusion moiety islinked in-frame to the polypeptide of the invention.

A signal sequence can be used to facilitate secretion and isolation ofmarker proteins. Signal sequences are typically characterized by a coreof hydrophobic amino acids which are generally cleaved from the matureprotein during secretion in one or more cleavage events. Such signalpeptides contain processing sites that allow cleavage of the signalsequence from the mature proteins as they pass through the secretorypathway. Thus, the invention pertains to marker proteins, fusionproteins or segments thereof having a signal sequence, as well as tosuch proteins from which the signal sequence has been proteolyticallycleaved (i.e., the cleavage products). In one embodiment, a nucleic acidsequence encoding a signal sequence can be operably linked in anexpression vector to a protein of interest, such as a marker protein ora segment thereof. The signal sequence directs secretion of the protein,such as from a eukaryotic host into which the expression vector istransformed, and the signal sequence is subsequently or concurrentlycleaved. The protein can then be readily purified from the extracellularmedium by art recognized methods. Alternatively, the signal sequence canbe linked to the protein of interest using a sequence which facilitatespurification, such as with a GST domain.

The present invention also pertains to variants of the marker proteins.Such variants have an altered amino acid sequence which can function aseither agonists (mimetics) or as antagonists. Variants can be generatedby mutagenesis, e.g., discrete point mutation or truncation. An agonistcan retain substantially the same, or a subset, of the biologicalactivities of the naturally occurring form of the protein. An antagonistof a protein can inhibit one or more of the activities of the naturallyoccurring form of the protein by, for example, competitively binding toa downstream or upstream member of a cellular signaling cascade whichincludes the protein of interest. Thus, specific biological effects canbe elicited by treatment with a variant of limited function. Treatmentof a subject with a variant having a subset of the biological activitiesof the naturally occurring form of the protein can have fewer sideeffects in a subject relative to treatment with the naturally occurringform of the protein.

Variants of a marker protein which function as either agonists(mimetics) or as antagonists can be identified by screeningcombinatorial libraries of mutants, e.g., truncation mutants, of theprotein of the invention for agonist or antagonist activity. In oneembodiment, a variegated library of variants is generated bycombinatorial mutagenesis at the nucleic acid level and is encoded by avariegated gene library. A variegated library of variants can beproduced by, for example, enzymatically ligating a mixture of syntheticoligonucleotides into gene sequences such that a degenerate set ofpotential protein sequences is expressible as individual polypeptides,or alternatively, as a set of larger fusion proteins (e.g., for phagedisplay). There are a variety of methods which can be used to producelibraries of potential variants of the marker proteins from a degenerateoligonucleotide sequence. Methods for synthesizing degenerateoligonucleotides are known in the art (see, e.g., Narang, 1983,Tetrahedron 39:3; Itakura et al., 1984, Annu. Rev. Biochem. 53:323;Itakura et al., 1984, Science 198:1056; Ike et al., 1983 Nucleic AcidRes. 11:477).

In addition, libraries of segments of a marker protein can be used togenerate a variegated population of polypeptides for screening andsubsequent selection of variant marker proteins or segments thereof. Forexample, a library of coding sequence fragments can be generated bytreating a double stranded PCR fragment of the coding sequence ofinterest with a nuclease under conditions wherein nicking occurs onlyabout once per molecule, denaturing the double stranded DNA, renaturingthe DNA to form double stranded DNA which can include sense/antisensepairs from different nicked products, removing single stranded portionsfrom reformed duplexes by treatment with S1 nuclease, and ligating theresulting fragment library into an expression vector. By this method, anexpression library can be derived which encodes amino terminal andinternal fragments of various sizes of the protein of interest.

Several techniques are known in the art for screening gene products ofcombinatorial libraries made by point mutations or truncation, and forscreening cDNA libraries for gene products having a selected property.The most widely used techniques, which are amenable to high through-putanalysis, for screening large gene libraries typically include cloningthe gene library into replicable expression vectors, transformingappropriate cells with the resulting library of vectors, and expressingthe combinatorial genes under conditions in which detection of a desiredactivity facilitates isolation of the vector encoding the gene whoseproduct was detected. Recursive ensemble mutagenesis (REM), a techniquewhich enhances the frequency of functional mutants in the libraries, canbe used in combination with the screening assays to identify variants ofa protein of the invention (Arkin and Yourvan, 1992, Proc. Natl. Acad.Sci. USA 89:7811-7815; Delgrave et al., 1993, Protein Engineering6(3):327-331).

Another aspect of the invention pertains to antibodies directed againsta protein of the invention. In preferred embodiments, the antibodiesspecifically bind a marker protein or a fragment thereof. The terms“antibody” and “antibodies” as used interchangeably herein refer toimmunoglobulin molecules as well as fragments and derivatives thereofthat comprise an immunologically active portion of an immunoglobulinmolecule, (i.e., such a portion contains an antigen binding site whichspecifically binds an antigen, such as a marker protein, e.g., anepitope of a marker protein). An antibody which specifically binds to aprotein of the invention is an antibody which binds the protein, butdoes not substantially bind other molecules in a sample, e.g., abiological sample, which naturally contains the protein. Examples of animmunologically active portion of an immunoglobulin molecule include,but are not limited to, single-chain antibodies (scAb), F(ab) andF(ab′)₂ fragments.

An isolated protein of the invention or a fragment thereof can be usedas an immunogen to generate antibodies. The full-length protein can beused or, alternatively, the invention provides antigenic peptidefragments for use as immunogens. The antigenic peptide of a protein ofthe invention comprises at least 8 (preferably 10, 15, 20, or 30 ormore) amino acid residues of the amino acid sequence of one of theproteins of the invention, and encompasses at least one epitope of theprotein such that an antibody raised against the peptide forms aspecific immune complex with the protein. Preferred epitopes encompassedby the antigenic peptide are regions that are located on the surface ofthe protein, e.g., hydrophilic regions. Hydrophobicity sequenceanalysis, hydrophilicity sequence analysis, or similar analyses can beused to identify hydrophilic regions. In preferred embodiments, anisolated marker protein or fragment thereof is used as an immunogen.

An immunogen typically is used to prepare antibodies by immunizing asuitable (i e immunocompetent) subject such as a rabbit, goat, mouse, orother mammal or vertebrate. An appropriate immunogenic preparation cancontain, for example, recombinantly-expressed or chemically-synthesizedprotein or peptide. The preparation can further include an adjuvant,such as Freund's complete or incomplete adjuvant, or a similarimmunostimulatory agent. Preferred immunogen compositions are those thatcontain no other human proteins such as, for example, immunogencompositions made using a non-human host cell for recombinant expressionof a protein of the invention. In such a manner, the resulting antibodycompositions have reduced or no binding of human proteins other than aprotein of the invention.

The invention provides polyclonal and monoclonal antibodies. The term“monoclonal antibody” or “monoclonal antibody composition”, as usedherein, refers to a population of antibody molecules that contain onlyone species of an antigen binding site capable of immunoreacting with aparticular epitope. Preferred polyclonal and monoclonal antibodycompositions are ones that have been selected for antibodies directedagainst a protein of the invention. Particularly preferred polyclonaland monoclonal antibody preparations are ones that contain onlyantibodies directed against a marker protein or fragment thereof.

Polyclonal antibodies can be prepared by immunizing a suitable subjectwith a protein of the invention as an immunogen The antibody titer inthe immunized subject can be monitored over time by standard techniques,such as with an enzyme linked immunosorbent assay (ELISA) usingimmobilized polypeptide. At an appropriate time after immunization,e.g., when the specific antibody titers are highest, antibody-producingcells can be obtained from the subject and used to prepare monoclonalantibodies (mAb) by standard techniques, such as the hybridoma techniqueoriginally described by Kohler and Milstein (1975) Nature 256:495-497,the human B cell hybridoma technique (see Kozbor et al., 1983, Immunol.Today 4:72), the EBV-hybridoma technique (see Cole et al., pp. 77-96 InMonoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., 1985) ortrioma techniques. The technology for producing hybridomas is well known(see generally Current Protocols in Immunology, Coligan et al. ed., JohnWiley & Sons, New York, 1994). Hybridoma cells producing a monoclonalantibody of the invention are detected by screening the hybridomaculture supernatants for antibodies that bind the polypeptide ofinterest, e.g., using a standard ELISA assay.

Alternative to preparing monoclonal antibody-secreting hybridomas, amonoclonal antibody directed against a protein of the invention can beidentified and isolated by screening a recombinant combinatorialimmunoglobulin library (e.g., an antibody phage display library) withthe polypeptide of interest. Kits for generating and screening phagedisplay libraries are commercially available (e.g., the PharmaciaRecombinant Phage Antibody System, Catalog No. 27-9400-01; and theStratagene SurfZAP Phage Display Kit, Catalog No. 240612). Additionally,examples of methods and reagents particularly amenable for use ingenerating and screening antibody display library can be found in, forexample, U.S. Pat. No. 5,223,409; PCT Publication No. WO 92/18619; PCTPublication No. WO 91/17271; PCT Publication No. WO 92/20791; PCTPublication No. WO 92/15679; PCT Publication No. WO 93/01288; PCTPublication No. WO 92/01047; PCT Publication No. WO 92/09690; PCTPublication No. WO 90/02809; Fuchs et al. (1991) Bio/Technology9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse etal. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J.12:725-734.

The invention also provides recombinant antibodies that specificallybind a protein of the invention. In preferred embodiments, therecombinant antibodies specifically binds a marker protein or fragmentthereof. Recombinant antibodies include, but are not limited to,chimeric and humanized monoclonal antibodies, comprising both human andnon-human portions, single-chain antibodies and multi-specificantibodies. A chimeric antibody is a molecule in which differentportions are derived from different animal species, such as those havinga variable region derived from a murine mAb and a human immunoglobulinconstant region. (See, e.g., Cabilly et al., U.S. Pat. No. 4,816,567;and Boss et al., U.S. Pat. No. 4,816,397, which are incorporated hereinby reference in their entirety.) Single-chain antibodies have an antigenbinding site and consist of a single polypeptides. They can be producedby techniques known in the art, for example using methods described inLadner et. al U.S. Pat. No. 4,946,778 (which is incorporated herein byreference in its entirety); Bird et al., (1988) Science 242:423-426;Whitlow et al., (1991) Methods in Enzymology 2:1-9; Whitlow et al.,(1991) Methods in Enzymology 2:97-105; and Huston et al., (1991) Methodsin Enzymology Molecular Design and Modeling: Concepts and Applications203:46-88. Multi-specific antibodies are antibody molecules having atleast two antigen-binding sites that specifically bind differentantigens. Such molecules can be produced by techniques known in the art,for example using methods described in Segal, U.S. Pat. No. 4,676,980(the disclosure of which is incorporated herein by reference in itsentirety); Holliger et al., (1993) Proc. Natl. Acad. Sci. USA90:6444-6448; Whitlow et al., (1994) Protein Eng. 7:1017-1026 and U.S.Pat. No. 6,121,424.

Humanized antibodies are antibody molecules from non-human specieshaving one or more complementarity determining regions (CDRs) from thenon-human species and a framework region from a human immunoglobulinmolecule. (See, e.g., Queen, U.S. Pat. No. 5,585,089, which isincorporated herein by reference in its entirety.) Humanized monoclonalantibodies can be produced by recombinant DNA techniques known in theart, for example using methods described in PCT Publication No. WO87/02671; European Patent Application 184,187; European PatentApplication 171,496; European Patent Application 173,494; PCTPublication No. WO 86/01533; U.S. Pat. No. 4,816,567; European PatentApplication 125,023; Better et al. (1988) Science 240:1041-1043; Liu etal. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J.Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA84:214-218; Nishimura et al. (1987) Cancer Res. 47:999-1005; Wood et al.(1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst.80:1553-1559); Morrison (1985) Science 229:1202-1207; Oi et al. (1986)Bio/Techniques 4:214; U.S. Pat. No. 5,225,539; Jones et al. (1986)Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; andBeidler et al. (1988) J. Immunol. 141:4053-4060.

More particularly, humanized antibodies can be produced, for example,using transgenic mice which are incapable of expressing endogenousimmunoglobulin heavy and light chains genes, but which can express humanheavy and light chain genes. The transgenic mice are immunized in thenormal fashion with a selected antigen, e.g., all or a portion of apolypeptide corresponding to a marker of the invention. Monoclonalantibodies directed against the antigen can be obtained usingconventional hybridoma technology. The human immunoglobulin transgenesharbored by the transgenic mice rearrange during B cell differentiation,and subsequently undergo class switching and somatic mutation. Thus,using such a technique, it is possible to produce therapeutically usefulIgG, IgA and IgE antibodies. For an overview of this technology forproducing human antibodies, see Lonberg and Huszar (1995) Int. Rev.Immunol. 13:65-93). For a detailed discussion of this technology forproducing human antibodies and human monoclonal antibodies and protocolsfor producing such antibodies, see, e.g., U.S. Pat. No. 5,625,126; U.S.Pat. No. 5,633,425; U.S. Pat. No. 5,569,825; U.S. Pat. No. 5,661,016;and U.S. Pat. No. 5,545,806. In addition, companies such as Abgenix,Inc. (Freemont, Calif.), can be engaged to provide human antibodiesdirected against a selected antigen using technology similar to thatdescribed above.

Completely human antibodies which recognize a selected epitope can begenerated using a technique referred to as “guided selection.” In thisapproach a selected non-human monoclonal antibody, e.g., a murineantibody, is used to guide the selection of a completely human antibodyrecognizing the same epitope (Jespers et al., 1994, Bio/technology12:899-903).

The antibodies of the invention can be isolated after production (e.g.,from the blood or serum of the subject) or synthesis and furtherpurified by well-known techniques. For example, IgG antibodies can bepurified using protein A chromatography. Antibodies specific for aprotein of the invention can be selected or (e.g., partially purified)or purified by, e.g., affinity chromatography. For example, arecombinantly expressed and purified (or partially purified) protein ofthe invention is produced as described herein, and covalently ornon-covalently coupled to a solid support such as, for example, achromatography column. The column can then be used to affinity purifyantibodies specific for the proteins of the invention from a samplecontaining antibodies directed against a large number of differentepitopes, thereby generating a substantially purified antibodycomposition, i.e., one that is substantially free of contaminatingantibodies. By a substantially purified antibody composition is meant,in this context, that the antibody sample contains at most only 30% (bydry weight) of contaminating antibodies directed against epitopes otherthan those of the desired protein of the invention, and preferably atmost 20%, yet more preferably at most 10%, and most preferably at most5% (by dry weight) of the sample is contaminating antibodies. A purifiedantibody composition means that at least 99% of the antibodies in thecomposition are directed against the desired protein of the invention.

In a preferred embodiment, the substantially purified antibodies of theinvention may specifically bind to a signal peptide, a secretedsequence, an extracellular domain, a transmembrane or a cytoplasmicdomain or cytoplasmic membrane of a protein of the invention. In aparticularly preferred embodiment, the substantially purified antibodiesof the invention specifically bind to a secreted sequence or anextracellular domain of the amino acid sequences of a protein of theinvention. In a more preferred embodiment, the substantially purifiedantibodies of the invention specifically bind to a secreted sequence oran extracellular domain of the amino acid sequences of a marker protein.

An antibody directed against a protein of the invention can be used toisolate the protein by standard techniques, such as affinitychromatography or immunoprecipitation. Moreover, such an antibody can beused to detect the marker protein or fragment thereof (e.g., in acellular lysate or cell supernatant) in order to evaluate the level andpattern of expression of the marker. The antibodies can also be useddiagnostically to monitor protein levels in tissues or body fluids (e.g.in a breast-associated body fluid) as part of a clinical testingprocedure, e.g., to, for example, determine the efficacy of a giventreatment regimen. Detection can be facilitated by the use of anantibody derivative, which comprises an antibody of the inventioncoupled to a detectable substance. Examples of detectable substancesinclude various enzymes, prosthetic groups, fluorescent materials,luminescent materials, bioluminescent materials, and radioactivematerials. Examples of suitable enzymes include horseradish peroxidase,alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examplesof suitable prosthetic group complexes include streptavidin/biotin andavidin/biotin; examples of suitable fluorescent materials includeumbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine,dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; anexample of a luminescent material includes luminol; examples ofbioluminescent materials include luciferase, luciferin, and aequorin,and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or³H.

Antibodies of the invention may also be used as therapeutic agents intreating cancers. In a preferred embodiment, completely human antibodiesof the invention are used for therapeutic treatment of human cancerpatients, particularly those having a breast cancer. In anotherpreferred embodiment, antibodies that bind specifically to a markerprotein or fragment thereof are used for therapeutic treatment. Further,such therapeutic antibody may be an antibody derivative or immunotoxincomprising an antibody conjugated to a therapeutic moiety such as acytotoxin, a therapeutic agent or a radioactive metal ion. A cytotoxinor cytotoxic agent includes any agent that is detrimental to cells.Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide,emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine,colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione,mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone,glucocorticoids, procaine, tetracaine, lidocaine, propranolol, andpuromycin and analogs or homologs thereof. Therapeutic agents include,but are not limited to, antimetabolites (e.g., methotrexate,6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracildecarbazine), alkylating agents (e.g., mechlorethamine, thioepachlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU),cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycinC, and cis-dichlorodiamine platinum (II) (DDP) cisplatin),anthracyclines (e.g., daunorubicin (formerly daunomycin) anddoxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin),bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents(e.g., vincristine and vinblastine).

The conjugated antibodies of the invention can be used for modifying agiven biological response, for the drug moiety is not to be construed aslimited to classical chemical therapeutic agents. For example, the drugmoiety may be a protein or polypeptide possessing a desired biologicalactivity. Such proteins may include, for example, a toxin such asribosome-inhibiting protein (see Better et al., U.S. Pat. No. 6,146,631,the disclosure of which is incorporated herein in its entirety), abrin,ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such astumor necrosis factor, .alpha.-interferon, .beta.-interferon, nervegrowth factor, platelet derived growth factor, tissue plasminogenactivator; or, biological response modifiers such as, for example,lymphokines, interleukin-1 (“IL-1”), interleukin-2 (“IL-2”),interleukin-6 (“IL-6”), granulocyte macrophase colony stimulating factor(“GM-CSF”), granulocyte colony stimulating factor (“G-CSF”), or othergrowth factors.

Techniques for conjugating such therapeutic moiety to antibodies arewell known, see, e.g., Arnon et al., “Monoclonal Antibodies ForImmunotargeting Of Drugs In Cancer Therapy”, in Monoclonal AntibodiesAnd Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss,Inc. 1985); Hellstrom et al., “Antibodies For Drug Delivery”, inControlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53(Marcel Dekker, Inc. 1987); Thorpe, “Antibody Carriers Of CytotoxicAgents In Cancer Therapy: A Review”, in Monoclonal Antibodies '84:Biological And Clinical Applications, Pinchera et al. (eds.), pp.475-506 (1985); “Analysis, Results, And Future Prospective Of TheTherapeutic Use Of Radiolabeled Antibody In Cancer Therapy”, inMonoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al.(eds.), pp. 303-16 (Academic Press 1985), and Thorpe et al., “ThePreparation And Cytotoxic Properties Of Antibody-Toxin Conjugates”,Immunol. Rev., 62:119-58 (1982).

Accordingly, in one aspect, the invention provides substantiallypurified antibodies, antibody fragments and derivatives, all of whichspecifically bind to a protein of the invention and preferably, a markerprotein. In various embodiments, the substantially purified antibodiesof the invention, or fragments or derivatives thereof, can be human,non-human, chimeric and/or humanized antibodies. In another aspect, theinvention provides non-human antibodies, antibody fragments andderivatives, all of which specifically bind to a protein of theinvention and preferably, a marker protein. Such non-human antibodiescan be goat, mouse, sheep, horse, chicken, rabbit, or rat antibodies.Alternatively, the non-human antibodies of the invention can be chimericand/or humanized antibodies. In addition, the non-human antibodies ofthe invention can be polyclonal antibodies or monoclonal antibodies. Instill a further aspect, the invention provides monoclonal antibodies,antibody fragments and derivatives, all of which specifically bind to aprotein of the invention and preferably, a marker protein. Themonoclonal antibodies can be human, humanized, chimeric and/or non-humanantibodies.

The invention also provides a kit containing an antibody of theinvention conjugated to a detectable substance, and instructions foruse. Still another aspect of the invention is a pharmaceuticalcomposition comprising an antibody of the invention and apharmaceutically acceptable carrier. In one embodiment, thepharmaceutical composition comprises an antibody of the invention, atherapeutic moiety, and a pharmaceutically acceptable carrier.

III. Recombinant Expression Vectors and Host Cells

Another aspect of the invention pertains to vectors, preferablyexpression vectors, containing a nucleic acid encoding a marker protein(or a portion of such a protein). As used herein, the term “vector”refers to a nucleic acid molecule capable of transporting anothernucleic acid to which it has been linked. One type of vector is a“plasmid”, which refers to a circular double stranded DNA loop intowhich additional DNA segments can be ligated. Another type of vector isa viral vector, wherein additional DNA segments can be ligated into theviral genome. Certain vectors are capable of autonomous replication in ahost cell into which they are introduced (e.g., bacterial vectors havinga bacterial origin of replication and episomal mammalian vectors). Othervectors (e.g., non-episomal mammalian vectors) are integrated into thegenome of a host cell upon introduction into the host cell, and therebyare replicated along with the host genome. Moreover, certain vectors,namely expression vectors, are capable of directing the expression ofgenes to which they are operably linked. In general, expression vectorsof utility in recombinant DNA techniques are often in the form ofplasmids (vectors). However, the invention is intended to include suchother forms of expression vectors, such as viral vectors (e.g.,replication defective retroviruses, adenoviruses and adeno-associatedviruses), which serve equivalent functions.

The recombinant expression vectors of the invention comprise a nucleicacid of the invention in a form suitable for expression of the nucleicacid in a host cell. This means that the recombinant expression vectorsinclude one or more regulatory sequences, selected on the basis of thehost cells to be used for expression, which is operably linked to thenucleic acid sequence to be expressed. Within a recombinant expressionvector, “operably linked” is intended to mean that the nucleotidesequence of interest is linked to the regulatory sequence(s) in a mannerwhich allows for expression of the nucleotide sequence (e.g., in an invitro transcription/translation system or in a host cell when the vectoris introduced into the host cell). The term “regulatory sequence” isintended to include promoters, enhancers and other expression controlelements (e.g., polyadenylation signals). Such regulatory sequences aredescribed, for example, in Goeddel, Methods in Enzymology: GeneExpression Technology vol. 185, Academic Press, San Diego, Calif.(1991). Regulatory sequences include those which direct constitutiveexpression of a nucleotide sequence in many types of host cell and thosewhich direct expression of the nucleotide sequence only in certain hostcells (e.g., tissue-specific regulatory sequences). It will beappreciated by those skilled in the art that the design of theexpression vector can depend on such factors as the choice of the hostcell to be transformed, the level of expression of protein desired, andthe like. The expression vectors of the invention can be introduced intohost cells to thereby produce proteins or peptides, including fusionproteins or peptides, encoded by nucleic acids as described herein.

The recombinant expression vectors of the invention can be designed forexpression of a marker protein or a segment thereof in prokaryotic(e.g., E. coli) or eukaryotic cells (e.g., insect cells {usingbaculovirus expression vectors}, yeast cells or mammalian cells).Suitable host cells are discussed further in Goeddel, supra.Alternatively, the recombinant expression vector can be transcribed andtranslated in vitro, for example using T7 promoter regulatory sequencesand T7 polymerase.

Expression of proteins in prokaryotes is most often carried out in E.coli with vectors containing constitutive or inducible promotersdirecting the expression of either fusion or non-fusion proteins. Fusionvectors add a number of amino acids to a protein encoded therein,usually to the amino terminus of the recombinant protein. Such fusionvectors typically serve three purposes: 1) to increase expression ofrecombinant protein; 2) to increase the solubility of the recombinantprotein; and 3) to aid in the purification of the recombinant protein byacting as a ligand in affinity purification. Often, in fusion expressionvectors, a proteolytic cleavage site is introduced at the junction ofthe fusion moiety and the recombinant protein to enable separation ofthe recombinant protein from the fusion moiety subsequent topurification of the fusion protein. Such enzymes, and their cognaterecognition sequences, include Factor Xa, thrombin and enterokinase.Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc;Smith and Johnson, 1988, Gene 67:31-40), pMAL (New England Biolabs,Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuseglutathione S-transferase (GST), maltose E binding protein, or proteinA, respectively, to the target recombinant protein.

Examples of suitable inducible non-fusion E. coli expression vectorsinclude pTrc (Amann et al., 1988, Gene 69:301-315) and pET 11d (Studieret al., p. 60-89, In Gene Expression Technology: Methods in Enzymologyvol. 185, Academic Press, San Diego, Calif., 1991). Target geneexpression from the pTrc vector relies on host RNA polymerasetranscription from a hybrid trp-lac fusion promoter. Target geneexpression from the pET 11d vector relies on transcription from a T7gn10-lac fusion promoter mediated by a co-expressed viral RNA polymerase(T7 gn1). This viral polymerase is supplied by host strains BL21(DE3) orHMS174(DE3) from a resident prophage harboring a T7 gn1 gene under thetranscriptional control of the lacUV 5 promoter.

One strategy to maximize recombinant protein expression in E. coli is toexpress the protein in a host bacteria with an impaired capacity toproteolytically cleave the recombinant protein (Gottesman, p. 119-128,In Gene Expression Technology: Methods in Enzymology vol. 185, AcademicPress, San Diego, Calif., 1990. Another strategy is to alter the nucleicacid sequence of the nucleic acid to be inserted into an expressionvector so that the individual codons for each amino acid are thosepreferentially utilized in E. coli (Wada et al., 1992, Nucleic AcidsRes. 20:2111-2118). Such alteration of nucleic acid sequences of theinvention can be carried out by standard DNA synthesis techniques.

In another embodiment, the expression vector is a yeast expressionvector. Examples of vectors for expression in yeast S. cerevisiaeinclude pYepSec1 (Baldari et al., 1987, EMBO J. 6:229-234), pMFa (Kurjanand Herskowitz, 1982, Cell 30:933-943), pJRY88 (Schultz et al., 1987,Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), andpPicZ (Invitrogen Corp, San Diego, Calif.).

Alternatively, the expression vector is a baculovirus expression vector.Baculovirus vectors available for expression of proteins in culturedinsect cells (e.g., Sf 9 cells) include the pAc series (Smith et al.,1983, Mol. Cell. Biol. 3:2156-2165) and the pVL series (Lucklow andSummers, 1989, Virology 170:31-39).

In yet another embodiment, a nucleic acid of the invention is expressedin mammalian cells using a mammalian expression vector. Examples ofmammalian expression vectors include pCDM8 (Seed, 1987, Nature 329:840)and pMT2PC (Kaufman et al., 1987, EMBO J. 6:187-195). When used inmammalian cells, the expression vector's control functions are oftenprovided by viral regulatory elements. For example, commonly usedpromoters are derived from polyoma, Adenovirus 2, cytomegalovirus andSimian Virus 40. For other suitable expression systems for bothprokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook etal., supra.

In another embodiment, the recombinant mammalian expression vector iscapable of directing expression of the nucleic acid preferentially in aparticular cell type (e.g., tissue-specific regulatory elements are usedto express the nucleic acid). Tissue-specific regulatory elements areknown in the art. Non-limiting examples of suitable tissue-specificpromoters include the albumin promoter (liver-specific; Pinkert et al.,1987, Genes Dev. 1:268-277), lymphoid-specific promoters (Calame andEaton, 1988, Adv. Immunol. 43:235-275), in particular promoters of Tcell receptors (Winoto and Baltimore, 1989, EMBO J. 8:729-733) andimmunoglobulins (Banerji et al., 1983, Cell 33:729-740; Queen andBaltimore, 1983, Cell 33:741-748), neuron-specific promoters (e.g., theneurofilament promoter; Byrne and Ruddle, 1989, Proc. Natl. Acad. Sci.USA 86:5473-5477), pancreas-specific promoters (Edlund et al., 1985,Science 230:912-916), and mammary gland-specific promoters (e.g., milkwhey promoter; U.S. Pat. No. 4,873,316 and European ApplicationPublication No. 264,166). Developmentally-regulated promoters are alsoencompassed, for example the murine hox promoters (Kessel and Gruss,1990, Science 249:374-379) and the α-fetoprotein promoter (Camper andTilghman, 1989, Genes Dev. 3:537-546).

The invention further provides a recombinant expression vectorcomprising a DNA molecule of the invention cloned into the expressionvector in an antisense orientation. That is, the DNA molecule isoperably linked to a regulatory sequence in a manner which allows forexpression (by transcription of the DNA molecule) of an RNA moleculewhich is antisense to the mRNA encoding a polypeptide of the invention.Regulatory sequences operably linked to a nucleic acid cloned in theantisense orientation can be chosen which direct the continuousexpression of the antisense RNA molecule in a variety of cell types, forinstance viral promoters and/or enhancers, or regulatory sequences canbe chosen which direct constitutive, tissue-specific or cell typespecific expression of antisense RNA. The antisense expression vectorcan be in the form of a recombinant plasmid, phagemid, or attenuatedvirus in which antisense nucleic acids are produced under the control ofa high efficiency regulatory region, the activity of which can bedetermined by the cell type into which the vector is introduced. For adiscussion of the regulation of gene expression using antisense genessee Weintraub et al., 1986, Trends in Genetics, Vol. 1(1).

Another aspect of the invention pertains to host cells into which arecombinant expression vector of the invention has been introduced. Theterms “host cell” and “recombinant host cell” are used interchangeablyherein. It is understood that such terms refer not only to theparticular subject cell but to the progeny or potential progeny of sucha cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

A host cell can be any prokaryotic (e.g., E. coli) or eukaryotic cell(e.g., insect cells, yeast or mammalian cells).

Vector DNA can be introduced into prokaryotic or eukaryotic cells viaconventional transformation or transfection techniques. As used herein,the terms “transformation” and “transfection” are intended to refer to avariety of art-recognized techniques for introducing foreign nucleicacid into a host cell, including calcium phosphate or calcium chlorideco-precipitation, DEAE-dextran-mediated transfection, lipofection, orelectroporation. Suitable methods for transforming or transfecting hostcells can be found in Sambrook, et al. (supra), and other laboratorymanuals.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign DNA into their genome. Inorder to identify and select these integrants, a gene that encodes aselectable marker (e.g., for resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest.Preferred selectable markers include those which confer resistance todrugs, such as G418, hygromycin and methotrexate. Cells stablytransfected with the introduced nucleic acid can be identified by drugselection (e.g., cells that have incorporated the selectable marker willsurvive, while the other cells die).

A host cell of the invention, such as a prokaryotic or eukaryotic hostcell in culture, can be used to produce a marker protein or a segmentthereof. Accordingly, the invention further provides methods forproducing a marker protein or a segment thereof using the host cells ofthe invention. In one embodiment, the method comprises culturing thehost cell of the invention (into which a recombinant expression vectorencoding a marker protein or a segment thereof has been introduced) in asuitable medium such that the is produced. In another embodiment, themethod further comprises isolating the a marker protein or a segmentthereof from the medium or the host cell.

The host cells of the invention can also be used to produce nonhumantransgenic animals. For example, in one embodiment, a host cell of theinvention is a fertilized oocyte or an embryonic stem cell into which asequences encoding a marker protein or a segment thereof have beenintroduced. Such host cells can then be used to create non-humantransgenic animals in which exogenous sequences encoding a markerprotein of the invention have been introduced into their genome orhomologous recombinant animals in which endogenous gene(s) encoding amarker protein have been altered. Such animals are useful for studyingthe function and/or activity of the marker protein and for identifyingand/or evaluating modulators of marker protein. As used herein, a“transgenic animal” is a non-human animal, preferably a mammal, morepreferably a rodent such as a rat or mouse, in which one or more of thecells of the animal includes a transgene. Other examples of transgenicanimals include non-human primates, sheep, dogs, cows, goats, chickens,amphibians, etc. A transgene is exogenous DNA which is integrated intothe genome of a cell from which a transgenic animal develops and whichremains in the genome of the mature animal, thereby directing theexpression of an encoded gene product in one or more cell types ortissues of the transgenic animal. As used herein, an “homologousrecombinant animal” is a non-human animal, preferably a mammal, morepreferably a mouse, in which an endogenous gene has been altered byhomologous recombination between the endogenous gene and an exogenousDNA molecule introduced into a cell of the animal, e.g., an embryoniccell of the animal, prior to development of the animal.

A transgenic animal of the invention can be created by introducing anucleic acid encoding a marker protein into the male pronuclei of afertilized oocyte, e.g., by microinjection, retroviral infection, andallowing the oocyte to develop in a pseudopregnant female foster animal.Intronic sequences and polyadenylation signals can also be included inthe transgene to increase the efficiency of expression of the transgene.A tissue-specific regulatory sequence(s) can be operably linked to thetransgene to direct expression of the polypeptide of the invention toparticular cells. Methods for generating transgenic animals via embryomanipulation and microinjection, particularly animals such as mice, havebecome conventional in the art and are described, for example, in U.S.Pat. Nos. 4,736,866 and 4,870,009, U.S. Pat. No. 4,873,191 and in Hogan,Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1986. Similar methods are used for production ofother transgenic animals. A transgenic founder animal can be identifiedbased upon the presence of the transgene in its genome and/or expressionof mRNA encoding the transgene in tissues or cells of the animals. Atransgenic founder animal can then be used to breed additional animalscarrying the transgene. Moreover, transgenic animals carrying thetransgene can further be bred to other transgenic animals carrying othertransgenes.

To create an homologous recombinant animal, a vector is prepared whichcontains at least a portion of a gene encoding a marker protein intowhich a deletion, addition or substitution has been introduced tothereby alter, e.g., functionally disrupt, the gene. In a preferredembodiment, the vector is designed such that, upon homologousrecombination, the endogenous gene is functionally disrupted (i.e., nolonger encodes a functional protein; also referred to as a “knock out”vector). Alternatively, the vector can be designed such that, uponhomologous recombination, the endogenous gene is mutated or otherwisealtered but still encodes functional protein (e.g., the upstreamregulatory region can be altered to thereby alter the expression of theendogenous protein). In the homologous recombination vector, the alteredportion of the gene is flanked at its 5′ and 3′ ends by additionalnucleic acid of the gene to allow for homologous recombination to occurbetween the exogenous gene carried by the vector and an endogenous genein an embryonic stem cell. The additional flanking nucleic acidsequences are of sufficient length for successful homologousrecombination with the endogenous gene. Typically, several kilobases offlanking DNA (both at the 5′ and 3′ ends) are included in the vector(see, e.g., Thomas and Capecchi, 1987, Cell 51:503 for a description ofhomologous recombination vectors). The vector is introduced into anembryonic stem cell line (e.g., by electroporation) and cells in whichthe introduced gene has homologously recombined with the endogenous geneare selected (see, e.g., Li et al., 1992, Cell 69:915). The selectedcells are then injected into a blastocyst of an animal (e.g., a mouse)to form aggregation chimeras (see, e.g., Bradley, Teratocarcinomas andEmbryonic Stem Cells: A Practical Approach, Robertson, Ed., IRL, Oxford,1987, pp. 113-152). A chimeric embryo can then be implanted into asuitable pseudopregnant female foster animal and the embryo brought toterm. Progeny harboring the homologously recombined DNA in their germcells can be used to breed animals in which all cells of the animalcontain the homologously recombined DNA by germline transmission of thetransgene. Methods for constructing homologous recombination vectors andhomologous recombinant animals are described further in Bradley (1991)Current Opinion in Bio/Technology 2:823-829 and in PCT Publication NOS.WO 90/11354, WO 91/01140, WO 92/0968, and WO 93/04169.

In another embodiment, transgenic non-human animals can be producedwhich contain selected systems which allow for regulated expression ofthe transgene. One example of such a system is the cre/loxP recombinasesystem of bacteriophage P1. For a description of the cre/loxPrecombinase system, see, e.g., Lakso et al. (1992) Proc. Natl. Acad.Sci. USA 89:6232-6236. Another example of a recombinase system is theFLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al.,1991, Science 251:1351-1355). If a cre/loxP recombinase system is usedto regulate expression of the transgene, animals containing transgenesencoding both the Cre recombinase and a selected protein are required.Such animals can be provided through the construction of “double”transgenic animals, e.g., by mating two transgenic animals, onecontaining a transgene encoding a selected protein and the othercontaining a transgene encoding a recombinase.

Clones of the non-human transgenic animals described herein can also beproduced according to the methods described in Wilmut et al. (1997)Nature 385:810-813 and PCT Publication NOS. WO 97/07668 and WO 97/07669.

IV. Pharmaceutical Compositions

The nucleic acid molecules, polypeptides, and antibodies (also referredto herein as “active compounds”) of the invention can be incorporatedinto pharmaceutical compositions suitable for administration. Suchcompositions typically comprise the nucleic acid molecule, protein, orantibody and a pharmaceutically acceptable carrier. As used herein thelanguage “pharmaceutically acceptable carrier” is intended to includeany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike, compatible with pharmaceutical administration. The use of suchmedia and agents for pharmaceutically active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active compound, use thereof in the compositionsis contemplated. Supplementary active compounds can also be incorporatedinto the compositions.

The invention includes methods for preparing pharmaceutical compositionsfor modulating the expression or activity of a marker nucleic acid orprotein. Such methods comprise formulating a pharmaceutically acceptablecarrier with an agent which modulates expression or activity of a markernucleic acid or protein. Such compositions can further includeadditional active agents. Thus, the invention further includes methodsfor preparing a pharmaceutical composition by formulating apharmaceutically acceptable carrier with an agent which modulatesexpression or activity of a marker nucleic acid or protein and one ormore additional active compounds.

The invention also provides methods (also referred to herein as“screening assays”) for identifying modulators, i.e., candidate or testcompounds or agents (e.g., peptides, peptidomimetics, peptoids, smallmolecules or other drugs) which (a) bind to the marker, or (b) have amodulatory (e.g., stimulatory or inhibitory) effect on the activity ofthe marker or, more specifically, (c) have a modulatory effect on theinteractions of the marker with one or more of its natural substrates(e.g., peptide, protein, hormone, co-factor, or nucleic acid), or (d)have a modulatory effect on the expression of the marker. Such assaystypically comprise a reaction between the marker and one or more assaycomponents. The other components may be either the test compound itself,or a combination of test compound and a natural binding partner of themarker.

The test compounds of the present invention may be obtained from anyavailable source, including systematic libraries of natural and/orsynthetic compounds. Test compounds may also be obtained by any of thenumerous approaches in combinatorial library methods known in the art,including: biological libraries; peptoid libraries (libraries ofmolecules having the functionalities of peptides, but with a novel,non-peptide backbone which are resistant to enzymatic degradation butwhich nevertheless remain bioactive; see, e.g., Zuckermann et al., 1994,J. Med. Chem. 37:2678-85); spatially addressable parallel solid phase orsolution phase libraries; synthetic library methods requiringdeconvolution; the ‘one-bead one-compound’ library method; and syntheticlibrary methods using affinity chromatography selection. The biologicallibrary and peptoid library approaches are limited to peptide libraries,while the other four approaches are applicable to peptide, non-peptideoligomer or small molecule libraries of compounds (Lam, 1997, AnticancerDrug Des. 12:145).

Examples of methods for the synthesis of molecular libraries can befound in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad.Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al.(1993) Science 261:1303; Carrell et al. (1994) Angew. Chem. Int. Ed.Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061;and in Gallop et al. (1994) J. Med. Chem. 37:1233.

Libraries of compounds may be presented in solution (e.g., Houghten,1992, Biotechniques 13:412-421), or on beads (Lam, 1991, Nature354:82-84), chips (Fodor, 1993, Nature 364:555-556), bacteria and/orspores, (Ladner, U.S. Pat. No. 5,223,409), plasmids (Cull et al, 1992,Proc Natl Acad Sci USA 89:1865-1869) or on phage (Scott and Smith, 1990,Science 249:386-390; Devlin, 1990, Science 249:404-406; Cwirla et al,1990, Proc. Natl. Acad. Sci. 87:6378-6382; Felici, 1991, J. Mol. Biol.222:301-310; Ladner, supra.).

In one embodiment, the invention provides assays for screening candidateor test compounds which are substrates of a protein encoded by orcorresponding to a marker or biologically active portion thereof. Inanother embodiment, the invention provides assays for screeningcandidate or test compounds which bind to a protein encoded by orcorresponding to a marker or biologically active portion thereof.Determining the ability of the test compound to directly bind to aprotein can be accomplished, for example, by coupling the compound witha radioisotope or enzymatic label such that binding of the compound tothe marker can be determined by detecting the labeled marker compound ina complex. For example, compounds (e.g., marker substrates) can belabeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, andthe radioisotope detected by direct counting of radioemission or byscintillation counting. Alternatively, assay components can beenzymatically labeled with, for example, horseradish peroxidase,alkaline phosphatase, or luciferase, and the enzymatic label detected bydetermination of conversion of an appropriate substrate to product.

In another embodiment, the invention provides assays for screeningcandidate or test compounds which modulate the expression of a marker orthe activity of a protein encoded by or corresponding to a marker, or abiologically active portion thereof. In all likelihood, the proteinencoded by or corresponding to the marker can, in vivo, interact withone or more molecules, such as but not limited to, peptides, proteins,hormones, cofactors and nucleic acids. For the purposes of thisdiscussion, such cellular and extracellular molecules are referred toherein as “binding partners” or marker “substrate”.

One necessary embodiment of the invention in order to facilitate suchscreening is the use of a protein encoded by or corresponding to markerto identify the protein's natural in vivo binding partners. There aremany ways to accomplish this which are known to one skilled in the art.One example is the use of the marker protein as “bait protein” in atwo-hybrid assay or three-hybrid assay (see, e.g., U.S. Pat. No.5,283,317; Zervos et al, 1993, Cell 72:223-232; Madura et al, 1993, J.Biol. Chem. 268:12046-12054; Bartel et al, 1993, Biotechniques14:920-924; Iwabuchi et al, 1993 Oncogene 8:1693-1696; Brent WO94/10300)in order to identify other proteins which bind to or interact with themarker (binding partners) and, therefore, are possibly involved in thenatural function of the marker. Such marker binding partners are alsolikely to be involved in the propagation of signals by the markerprotein or downstream elements of a marker protein-mediated signalingpathway. Alternatively, such marker protein binding partners may also befound to be inhibitors of the marker protein.

The two-hybrid system is based on the modular nature of mosttranscription factors, which consist of separable DNA-binding andactivation domains. Briefly, the assay utilizes two different DNAconstructs. In one construct, the gene that encodes a marker proteinfused to a gene encoding the DNA binding domain of a known transcriptionfactor (e.g., GAL-4). In the other construct, a DNA sequence, from alibrary of DNA sequences, that encodes an unidentified protein (“prey”or “sample”) is fused to a gene that codes for the activation domain ofthe known transcription factor. If the “bait” and the “prey” proteinsare able to interact, in vivo, forming a marker-dependent complex, theDNA-binding and activation domains of the transcription factor arebrought into close proximity. This proximity allows transcription of areporter gene (e.g., LacZ) which is operably linked to a transcriptionalregulatory site responsive to the transcription factor. Expression ofthe reporter gene can be readily detected and cell colonies containingthe functional transcription factor can be isolated and used to obtainthe cloned gene which encodes the protein which interacts with themarker protein.

In a further embodiment, assays may be devised through the use of theinvention for the purpose of identifying compounds which modulate (e.g.,affect either positively or negatively) interactions between a markerprotein and its substrates and/or binding partners. Such compounds caninclude, but are not limited to, molecules such as antibodies, peptides,hormones, oligonucleotides, nucleic acids, and analogs thereof. Suchcompounds may also be obtained from any available source, includingsystematic libraries of natural and/or synthetic compounds. Thepreferred assay components for use in this embodiment is a breast cancermarker protein identified herein, the known binding partner and/orsubstrate of same, and the test compound. Test compounds can be suppliedfrom any source.

The basic principle of the assay systems used to identify compounds thatinterfere with the interaction between the marker protein and itsbinding partner involves preparing a reaction mixture containing themarker protein and its binding partner under conditions and for a timesufficient to allow the two products to interact and bind, thus forminga complex. In order to test an agent for inhibitory activity, thereaction mixture is prepared in the presence and absence of the testcompound. The test compound can be initially included in the reactionmixture, or can be added at a time subsequent to the addition of themarker protein and its binding partner. Control reaction mixtures areincubated without the test compound or with a placebo. The formation ofany complexes between the marker protein and its binding partner is thendetected. The formation of a complex in the control reaction, but lessor no such formation in the reaction mixture containing the testcompound, indicates that the compound interferes with the interaction ofthe marker protein and its binding partner. Conversely, the formation ofmore complex in the presence of compound than in the control reactionindicates that the compound may enhance interaction of the markerprotein and its binding partner.

The assay for compounds that interfere with the interaction of themarker protein with its binding partner may be conducted in aheterogeneous or homogeneous format. Heterogeneous assays involveanchoring either the marker protein or its binding partner onto a solidphase and detecting complexes anchored to the solid phase at the end ofthe reaction. In homogeneous assays, the entire reaction is carried outin a liquid phase. In either approach, the order of addition ofreactants can be varied to obtain different information about thecompounds being tested. For example, test compounds that interfere withthe interaction between the marker proteins and the binding partners(e.g., by competition) can be identified by conducting the reaction inthe presence of the test substance, i.e., by adding the test substanceto the reaction mixture prior to or simultaneously with the marker andits interactive binding partner. Alternatively, test compounds thatdisrupt preformed complexes, e.g., compounds with higher bindingconstants that displace one of the components from the complex, can betested by adding the test compound to the reaction mixture aftercomplexes have been formed. The various formats are briefly describedbelow.

In a heterogeneous assay system, either the marker protein or itsbinding partner is anchored onto a solid surface or matrix, while theother corresponding non-anchored component may be labeled, eitherdirectly or indirectly. In practice, microtitre plates are oftenutilized for this approach. The anchored species can be immobilized by anumber of methods, either non-covalent or covalent, that are typicallywell known to one who practices the art. Non-covalent attachment canoften be accomplished simply by coating the solid surface with asolution of the marker protein or its binding partner and drying.Alternatively, an immobilized antibody specific for the assay componentto be anchored can be used for this purpose. Such surfaces can often beprepared in advance and stored.

In related embodiments, a fusion protein can be provided which adds adomain that allows one or both of the assay components to be anchored toa matrix. For example, glutathione-S-transferase/marker fusion proteinsor glutathione-S-transferase/binding partner can be adsorbed ontoglutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtiter plates, which are then combined withthe test compound or the test compound and either the non-adsorbedmarker or its binding partner, and the mixture incubated underconditions conducive to complex formation (e.g., physiologicalconditions). Following incubation, the beads or microtiter plate wellsare washed to remove any unbound assay components, the immobilizedcomplex assessed either directly or indirectly, for example, asdescribed above. Alternatively, the complexes can be dissociated fromthe matrix, and the level of marker binding or activity determined usingstandard techniques.

Other techniques for immobilizing proteins on matrices can also be usedin the screening assays of the invention. For example, either a markerprotein or a marker protein binding partner can be immobilized utilizingconjugation of biotin and streptavidin. Biotinylated marker protein ortarget molecules can be prepared from biotin-NHS(N-hydroxy-succinimide)using techniques known in the art (e.g., biotinylation kit, PierceChemicals, Rockford, Ill.), and immobilized in the wells ofstreptavidin-coated 96 well plates (Pierce Chemical). In certainembodiments, the protein-immobilized surfaces can be prepared in advanceand stored.

In order to conduct the assay, the corresponding partner of theimmobilized assay component is exposed to the coated surface with orwithout the test compound. After the reaction is complete, unreactedassay components are removed (e.g., by washing) and any complexes formedwill remain immobilized on the solid surface. The detection of complexesanchored on the solid surface can be accomplished in a number of ways.Where the non-immobilized component is pre-labeled, the detection oflabel immobilized on the surface indicates that complexes were formed.Where the non-immobilized component is not pre-labeled, an indirectlabel can be used to detect complexes anchored on the surface; e.g.,using a labeled antibody specific for the initially non-immobilizedspecies (the antibody, in turn, can be directly labeled or indirectlylabeled with, e.g., a labeled anti-Ig antibody). Depending upon theorder of addition of reaction components, test compounds which modulate(inhibit or enhance) complex formation or which disrupt preformedcomplexes can be detected.

In an alternate embodiment of the invention, a homogeneous assay may beused. This is typically a reaction, analogous to those mentioned above,which is conducted in a liquid phase in the presence or absence of thetest compound. The formed complexes are then separated from unreactedcomponents, and the amount of complex formed is determined. As mentionedfor heterogeneous assay systems, the order of addition of reactants tothe liquid phase can yield information about which test compoundsmodulate (inhibit or enhance) complex formation and which disruptpreformed complexes.

In such a homogeneous assay, the reaction products may be separated fromunreacted assay components by any of a number of standard techniques,including but not limited to: differential centrifugation,chromatography, electrophoresis and immunoprecipitation. In differentialcentrifugation, complexes of molecules may be separated from uncomplexedmolecules through a series of centrifugal steps, due to the differentsedimentation equilibria of complexes based on their different sizes anddensities (see, for example, Rivas, G., and Minton, A. P., TrendsBiochem Sci 1993 August; 18(8):284-7). Standard chromatographictechniques may also be utilized to separate complexed molecules fromuncomplexed ones. For example, gel filtration chromatography separatesmolecules based on size, and through the utilization of an appropriategel filtration resin in a column format, for example, the relativelylarger complex may be separated from the relatively smaller uncomplexedcomponents. Similarly, the relatively different charge properties of thecomplex as compared to the uncomplexed molecules may be exploited todifferentially separate the complex from the remaining individualreactants, for example through the use of ion-exchange chromatographyresins. Such resins and chromatographic techniques are well known to oneskilled in the art (see, e.g., Heegaard, 1998, J. Mol. Recognit.11:141-148; Hage and Tweed, 1997, J. Chromatogr. B. Biomed. Sci. Appl.,699:499-525). Gel electrophoresis may also be employed to separatecomplexed molecules from unbound species (see, e.g., Ausubel et al(eds.), In: Current Protocols in Molecular Biology, J. Wiley & Sons, NewYork. 1999). In this technique, protein or nucleic acid complexes areseparated based on size or charge, for example. In order to maintain thebinding interaction during the electrophoretic process, nondenaturinggels in the absence of reducing agent are typically preferred, butconditions appropriate to the particular interactants will be well knownto one skilled in the art. Immunoprecipitation is another commontechnique utilized for the isolation of a protein-protein complex fromsolution (see, e.g., Ausubel et al (eds.), In: Current Protocols inMolecular Biology, J. Wiley & Sons, New York. 1999). In this technique,all proteins binding to an antibody specific to one of the bindingmolecules are precipitated from solution by conjugating the antibody toa polymer bead that may be readily collected by centrifugation. Thebound assay components are released from the beads (through a specificproteolysis event or other technique well known in the art which willnot disturb the protein-protein interaction in the complex), and asecond immunoprecipitation step is performed, this time utilizingantibodies specific for the correspondingly different interacting assaycomponent. In this manner, only formed complexes should remain attachedto the beads. Variations in complex formation in both the presence andthe absence of a test compound can be compared, thus offeringinformation about the ability of the compound to modulate interactionsbetween the marker protein and its binding partner.

Also within the scope of the present invention are methods for directdetection of interactions between the marker protein and its naturalbinding partner and/or a test compound in a homogeneous or heterogeneousassay system without further sample manipulation. For example, thetechnique of fluorescence energy transfer may be utilized (see, e.g.,Lakowicz et al, U.S. Pat. No. 5,631,169; Stavrianopoulos et al, U.S.Pat. No. 4,868,103). Generally, this technique involves the addition ofa fluorophore label on a first ‘donor’ molecule (e.g., marker or testcompound) such that its emitted fluorescent energy will be absorbed by afluorescent label on a second, ‘acceptor’ molecule (e.g., marker or testcompound), which in turn is able to fluoresce due to the absorbedenergy. Alternately, the ‘donor’ protein molecule may simply utilize thenatural fluorescent energy of tryptophan residues. Labels are chosenthat emit different wavelengths of light, such that the ‘acceptor’molecule label may be differentiated from that of the ‘donor’. Since theefficiency of energy transfer between the labels is related to thedistance separating the molecules, spatial relationships between themolecules can be assessed. In a situation in which binding occursbetween the molecules, the fluorescent emission of the ‘acceptor’molecule label in the assay should be maximal. An FET binding event canbe conveniently measured through standard fluorometric detection meanswell known in the art (e.g., using a fluorimeter). A test substancewhich either enhances or hinders participation of one of the species inthe preformed complex will result in the generation of a signal variantto that of background. In this way, test substances that modulateinteractions between a marker and its binding partner can be identifiedin controlled assays.

In another embodiment, modulators of marker expression are identified ina method wherein a cell is contacted with a candidate compound and theexpression of marker mRNA or protein in the cell, is determined. Thelevel of expression of marker mRNA or protein in the presence of thecandidate compound is compared to the level of expression of marker mRNAor protein in the absence of the candidate compound. The candidatecompound can then be identified as a modulator of marker expressionbased on this comparison. For example, when expression of marker mRNA orprotein is greater (statistically significantly greater) in the presenceof the candidate compound than in its absence, the candidate compound isidentified as a stimulator of marker mRNA or protein expression.Conversely, when expression of marker mRNA or protein is less(statistically significantly less) in the presence of the candidatecompound than in its absence, the candidate compound is identified as aninhibitor of marker mRNA or protein expression. The level of marker mRNAor protein expression in the cells can be determined by methodsdescribed herein for detecting marker mRNA or protein.

In another aspect, the invention pertains to a combination of two ormore of the assays described herein. For example, a modulating agent canbe identified using a cell-based or a cell free assay, and the abilityof the agent to modulate the activity of a marker protein can be furtherconfirmed in vivo, e.g., in a whole animal model for cellulartransformation and/or tumorigenesis.

This invention further pertains to novel agents identified by theabove-described screening assays. Accordingly, it is within the scope ofthis invention to further use an agent identified as described herein inan appropriate animal model. For example, an agent identified asdescribed herein (e.g., an marker modulating agent, an antisense markernucleic acid molecule, an marker-specific antibody, or an marker-bindingpartner) can be used in an animal model to determine the efficacy,toxicity, or side effects of treatment with such an agent.Alternatively, an agent identified as described herein can be used in ananimal model to determine the mechanism of action of such an agent.Furthermore, this invention pertains to uses of novel agents identifiedby the above-described screening assays for treatments as describedherein.

It is understood that appropriate doses of small molecule agents andprotein or polypeptide agents depends upon a number of factors withinthe knowledge of the ordinarily skilled physician, veterinarian, orresearcher. The dose(s) of these agents will vary, for example,depending upon the identity, size, and condition of the subject orsample being treated, further depending upon the route by which thecomposition is to be administered, if applicable, and the effect whichthe practitioner desires the agent to have upon the nucleic acid orpolypeptide of the invention. Exemplary doses of a small moleculeinclude milligram or microgram amounts per kilogram of subject or sampleweight (e.g. about 1 microgram per kilogram to about 500 milligrams perkilogram, about 100 micrograms per kilogram to about 5 milligrams perkilogram, or about 1 microgram per kilogram to about 50 micrograms perkilogram). Exemplary doses of a protein or polypeptide include gram,milligram or microgram amounts per kilogram of subject or sample weight(e.g. about 1 microgram per kilogram to about 5 grams per kilogram,about 100 micrograms per kilogram to about 500 milligrams per kilogram,or about 1 milligram per kilogram to about 50 milligrams per kilogram).It is furthermore understood that appropriate doses of one of theseagents depend upon the potency of the agent with respect to theexpression or activity to be modulated. Such appropriate doses can bedetermined using the assays described herein. When one or more of theseagents is to be administered to an animal (e.g. a human) in order tomodulate expression or activity of a polypeptide or nucleic acid of theinvention, a physician, veterinarian, or researcher can, for example,prescribe a relatively low dose at first, subsequently increasing thedose until an appropriate response is obtained. In addition, it isunderstood that the specific dose level for any particular animalsubject will depend upon a variety of factors including the activity ofthe specific agent employed, the age, body weight, general health,gender, and diet of the subject, the time of administration, the routeof administration, the rate of excretion, any drug combination, and thedegree of expression or activity to be modulated.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation), transdermal (topical),transmucosal, and rectal administration. Solutions or suspensions usedfor parenteral, intradermal, or subcutaneous application can include thefollowing components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediamine-tetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampules,disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersions. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEL (BASF; Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride inthe composition. Prolonged absorption of the injectable compositions canbe brought about by including in the composition an agent which delaysabsorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the activecompound (e.g., a polypeptide or antibody) in the required amount in anappropriate solvent with one or a combination of ingredients enumeratedabove, as required, followed by filtered sterilization. Generally,dispersions are prepared by incorporating the active compound into asterile vehicle which contains a basic dispersion medium, and thenincorporating the required other ingredients from those enumeratedabove. In the case of sterile powders for the preparation of sterileinjectable solutions, the preferred methods of preparation are vacuumdrying and freeze-drying which yields a powder of the active ingredientplus any additional desired ingredient from a previouslysterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Oral compositions can also be preparedusing a fluid carrier for use as a mouthwash, wherein the compound inthe fluid carrier is applied orally and swished and expectorated orswallowed.

Pharmaceutically compatible binding agents, and/or adjuvant materialscan be included as part of the composition. The tablets, pills,capsules, troches, and the like can contain any of the followingingredients, or compounds of a similar nature: a binder such asmicrocrystalline cellulose, gum tragacanth or gelatin; an excipient suchas starch or lactose, a disintegrating agent such as alginic acid,Primogel, or corn starch; a lubricant such as magnesium stearate orSterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from a pressurized container or dispenser whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration, detergents, bile salts, andfusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g.,with conventional suppository bases such as cocoa butter and otherglycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers thatwill protect the compound against rapid elimination from the body, suchas a controlled release formulation, including implants andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes having monoclonal antibodies incorporated thereinor thereon) can also be used as pharmaceutically acceptable carriers.These can be prepared according to methods known to those skilled in theart, for example, as described in U.S. Pat. No. 4,522,811.

It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved, and the limitationsinherent in the art of compounding such an active compound for thetreatment of individuals.

For antibodies, the preferred dosage is 0.1 mg/kg to 100 mg/kg of bodyweight (generally 10 mg/kg to 20 mg/kg). If the antibody is to act inthe brain, a dosage of 50 mg/kg to 100 mg/kg is usually appropriate.Generally, partially human antibodies and fully human antibodies have alonger half-life within the human body than other antibodies.Accordingly, lower dosages and less frequent administration is oftenpossible. Modifications such as lipidation can be used to stabilizeantibodies and to enhance uptake and tissue penetration. A method forlipidation of antibodies is described by Cruikshank et al. (1997) J.Acquired Immune Deficiency Syndromes and Human Retrovirology 14:193.

The invention also provides vaccine compositions for the preventionand/or treatment of breast cancer. The invention provides breast cancervaccine compositions in which a protein of a marker of Table 1, or acombination of proteins of the markers of Table 1, are introduced into asubject in order to stimulate an immune response against the breastcancer. The invention also provides breast cancer vaccine compositionsin which a gene expression construct, which expresses a marker orfragment of a marker identified in Table 1, is introduced into thesubject such that a protein or fragment of a protein encoded by a markerof Table 1 is produced by transfected cells in the subject at a higherthan normal level and elicits an immune response.

In one embodiment, a breast cancer vaccine is provided and employed asan immunotherapeutic agent for the prevention of breast cancer. Inanother embodiment, a breast cancer vaccine is provided and employed asan immunotherapeutic agent for the treatment of breast cancer.

By way of example, a breast cancer vaccine comprised of the proteins ofthe markers of Table 1, may be employed for the prevention and/ortreatment of breast cancer in a subject by administering the vaccine bya variety of routes, e.g., intradermally, subcutaneously, orintramuscularly. In addition, the breast cancer vaccine can beadministered together with adjuvants and/or immunomodulators to boostthe activity of the vaccine and the subject's response. In oneembodiment, devices and/or compositions containing the vaccine, suitablefor sustained or intermittent release could be, implanted in the body ortopically applied thereto for the relatively slow release of suchmaterials into the body. The breast cancer vaccine can be introducedalong with immunomodulatory compounds, which can alter the type ofimmune response produced in order to produce a response which will bemore effective in eliminating the cancer.

In another embodiment, a breast cancer vaccine comprised of anexpression construct of the markers of Table 1, may be introduced byinjection into muscle or by coating onto microprojectiles and using adevice designed for the purpose to fire the projectiles at high speedinto the skin. The cells of the subject will then express the protein(s)or fragments of proteins of the markers of Table 1 and induce an immuneresponse. In addition, the breast cancer vaccine may be introduced alongwith expression constructs for immunomodulatory molecules, such ascytokines, which may increase the immune response or modulate the typeof immune response produced in order to produce a response which will bemore effective in eliminating the cancer.

The marker nucleic acid molecules can be inserted into vectors and usedas gene therapy vectors. Gene therapy vectors can be delivered to asubject by, for example, intravenous injection, local administration(U.S. Pat. No. 5,328,470), or by stereotactic injection (see, e.g., Chenet al., 1994, Proc. Natl. Acad. Sci. USA 91:3054-3057). Thepharmaceutical preparation of the gene therapy vector can include thegene therapy vector in an acceptable diluent, or can comprise a slowrelease matrix in which the gene delivery vehicle is imbedded.Alternatively, where the complete gene delivery vector can be producedintact from recombinant cells, e.g. retroviral vectors, thepharmaceutical preparation can include one or more cells which producethe gene delivery system.

The pharmaceutical compositions can be included in a container, pack, ordispenser together with instructions for administration.

V. Predictive Medicine

The present invention pertains to the field of predictive medicine inwhich diagnostic assays, prognostic assays, pharmacogenomics, andmonitoring clinical trails are used for prognostic (predictive) purposesto thereby treat an individual prophylactically. Accordingly, one aspectof the present invention relates to diagnostic assays for determiningthe level of expression of one or more marker proteins or nucleic acids,in order to determine whether an individual is at risk of developingbreast cancer. Such assays can be used for prognostic or predictivepurposes to thereby prophylactically treat an individual prior to theonset of the cancer.

Yet another aspect of the invention pertains to monitoring the influenceof agents (e.g., drugs or other compounds administered either to inhibitbreast cancer or to treat or prevent any other disorder {i.e. in orderto understand any breast carcinogenic effects that such treatment mayhave}) on the expression or activity of a marker of the invention inclinical trials. These and other agents are described in further detailin the following sections.

A. Diagnostic Assays

An exemplary method for detecting the presence or absence of a markerprotein or nucleic acid in a biological sample involves obtaining abiological sample (e.g. a breast associated body fluid) from a testsubject and contacting the biological sample with a compound or an agentcapable of detecting the polypeptide or nucleic acid (e.g., mRNA,genomic DNA, or cDNA). The detection methods of the invention can thusbe used to detect mRNA, protein, cDNA, or genomic DNA, for example, in abiological sample in vitro as well as in vivo. For example, in vitrotechniques for detection of mRNA include Northern hybridizations and insitu hybridizations. In vitro techniques for detection of a markerprotein include enzyme linked immunosorbent assays (ELISAs), Westernblots, immunoprecipitations and immunofluorescence. In vitro techniquesfor detection of genomic DNA include Southern hybridizations.Furthermore, in vivo techniques for detection of a marker proteininclude introducing into a subject a labeled antibody directed againstthe protein or fragment thereof. For example, the antibody can belabeled with a radioactive marker whose presence and location in asubject can be detected by standard imaging techniques.

A general principle of such diagnostic and prognostic assays involvespreparing a sample or reaction mixture that may contain a marker, and aprobe, under appropriate conditions and for a time sufficient to allowthe marker and probe to interact and bind, thus forming a complex thatcan be removed and/or detected in the reaction mixture. These assays canbe conducted in a variety of ways.

For example, one method to conduct such an assay would involve anchoringthe marker or probe onto a solid phase support, also referred to as asubstrate, and detecting target marker/probe complexes anchored on thesolid phase at the end of the reaction. In one embodiment of such amethod, a sample from a subject, which is to be assayed for presenceand/or concentration of marker, can be anchored onto a carrier or solidphase support. In another embodiment, the reverse situation is possible,in which the probe can be anchored to a solid phase and a sample from asubject can be allowed to react as an unanchored component of the assay.

There are many established methods for anchoring assay components to asolid phase. These include, without limitation, marker or probemolecules which are immobilized through conjugation of biotin andstreptavidin. Such biotinylated assay components can be prepared frombiotin-NHS(N-hydroxy-succinimide) using techniques known in the art(e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), andimmobilized in the wells of streptavidin-coated 96 well plates (PierceChemical). In certain embodiments, the surfaces with immobilized assaycomponents can be prepared in advance and stored.

Other suitable carriers or solid phase supports for such assays includeany material capable of binding the class of molecule to which themarker or probe belongs. Well-known supports or carriers include, butare not limited to, glass, polystyrene, nylon, polypropylene, nylon,polyethylene, dextran, amylases, natural and modified celluloses,polyacrylamides, gabbros, and magnetite.

In order to conduct assays with the above mentioned approaches, thenon-immobilized component is added to the solid phase upon which thesecond component is anchored. After the reaction is complete,uncomplexed components may be removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized uponthe solid phase. The detection of marker/probe complexes anchored to thesolid phase can be accomplished in a number of methods outlined herein.

In a preferred embodiment, the probe, when it is the unanchored assaycomponent, can be labeled for the purpose of detection and readout ofthe assay, either directly or indirectly, with detectable labelsdiscussed herein and which are well-known to one skilled in the art.

It is also possible to directly detect marker/probe complex formationwithout further manipulation or labeling of either component (marker orprobe), for example by utilizing the technique of fluorescence energytransfer (see, for example, Lakowicz et al., U.S. Pat. No. 5,631,169;Stavrianopoulos, et al., U.S. Pat. No. 4,868,103). A fluorophore labelon the first, ‘donor’ molecule is selected such that, upon excitationwith incident light of appropriate wavelength, its emitted fluorescentenergy will be absorbed by a fluorescent label on a second ‘acceptor’molecule, which in turn is able to fluoresce due to the absorbed energy.Alternately, the ‘donor’ protein molecule may simply utilize the naturalfluorescent energy of tryptophan residues. Labels are chosen that emitdifferent wavelengths of light, such that the ‘acceptor’ molecule labelmay be differentiated from that of the ‘donor’. Since the efficiency ofenergy transfer between the labels is related to the distance separatingthe molecules, spatial relationships between the molecules can beassessed. In a situation in which binding occurs between the molecules,the fluorescent emission of the ‘acceptor’ molecule label in the assayshould be maximal. An FET binding event can be conveniently measuredthrough standard fluorometric detection means well known in the art(e.g., using a fluorimeter).

In another embodiment, determination of the ability of a probe torecognize a marker can be accomplished without labeling either assaycomponent (probe or marker) by utilizing a technology such as real-timeBiomolecular Interaction Analysis (BIA) (see, e.g., Sjolander, S, andUrbaniczky, C., 1991, Anal. Chem. 63:2338-2345 and Szabo et al., 1995,Curr. Opin. Struct. Biol. 5:699-705). As used herein, “BIA” or “surfaceplasmon resonance” is a technology for studying biospecific interactionsin real time, without labeling any of the interactants (e.g., BIAcore).Changes in the mass at the binding surface (indicative of a bindingevent) result in alterations of the refractive index of light near thesurface (the optical phenomenon of surface plasmon resonance (SPR)),resulting in a detectable signal which can be used as an indication ofreal-time reactions between biological molecules.

Alternatively, in another embodiment, analogous diagnostic andprognostic assays can be conducted with marker and probe as solutes in aliquid phase. In such an assay, the complexed marker and probe areseparated from uncomplexed components by any of a number of standardtechniques, including but not limited to: differential centrifugation,chromatography, electrophoresis and immunoprecipitation. In differentialcentrifugation, marker/probe complexes may be separated from uncomplexedassay components through a series of centrifugal steps, due to thedifferent sedimentation equilibria of complexes based on their differentsizes and densities (see, for example, Rivas, G., and Minton, A. P.,1993, Trends Biochem Sci. 18(8):284-7). Standard chromatographictechniques may also be utilized to separate complexed molecules fromuncomplexed ones. For example, gel filtration chromatography separatesmolecules based on size, and through the utilization of an appropriategel filtration resin in a column format, for example, the relativelylarger complex may be separated from the relatively smaller uncomplexedcomponents. Similarly, the relatively different charge properties of themarker/probe complex as compared to the uncomplexed components may beexploited to differentiate the complex from uncomplexed components, forexample through the utilization of ion-exchange chromatography resins.Such resins and chromatographic techniques are well known to one skilledin the art (see, e.g., Heegaard, N. H., 1998, J. Mol. Recognit. Winter11(1-6):141-8; Hage, D. S., and Tweed, S. A. J Chromatogr B Biomed SciAppl 1997 Oct. 10; 699(1-2):499-525). Gel electrophoresis may also beemployed to separate complexed assay components from unbound components(see, e.g., Ausubel et al., ed., Current Protocols in Molecular Biology,John Wiley & Sons, New York, 1987-1999). In this technique, protein ornucleic acid complexes are separated based on size or charge, forexample. In order to maintain the binding interaction during theelectrophoretic process, non-denaturing gel matrix materials andconditions in the absence of reducing agent are typically preferred.Appropriate conditions to the particular assay and components thereofwill be well known to one skilled in the art.

In a particular embodiment, the level of marker mRNA can be determinedboth by in situ and by in vitro formats in a biological sample usingmethods known in the art. The term “biological sample” is intended toinclude tissues, cells, biological fluids and isolates thereof, isolatedfrom a subject, as well as tissues, cells and fluids present within asubject. Many expression detection methods use isolated RNA. For invitro methods, any RNA isolation technique that does not select againstthe isolation of mRNA can be utilized for the purification of RNA frombreast cells (see, e.g., Ausubel et al., ed., Current Protocols inMolecular Biology, John Wiley & Sons, New York 1987-1999). Additionally,large numbers of tissue samples can readily be processed usingtechniques well known to those of skill in the art, such as, forexample, the single-step RNA isolation process of Chomczynski (1989,U.S. Pat. No. 4,843,155).

The isolated mRNA can be used in hybridization or amplification assaysthat include, but are not limited to, Southern or Northern analyses,polymerase chain reaction analyses and probe arrays. One preferreddiagnostic method for the detection of mRNA levels involves contactingthe isolated mRNA with a nucleic acid molecule (probe) that canhybridize to the mRNA encoded by the gene being detected. The nucleicacid probe can be, for example, a full-length cDNA, or a portionthereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250or 500 nucleotides in length and sufficient to specifically hybridizeunder stringent conditions to a mRNA or genomic DNA encoding a marker ofthe present invention. Other suitable probes for use in the diagnosticassays of the invention are described herein. Hybridization of an mRNAwith the probe indicates that the marker in question is being expressed.

In one format, the mRNA is immobilized on a solid surface and contactedwith a probe, for example by running the isolated mRNA on an agarose geland transferring the mRNA from the gel to a membrane, such asnitrocellulose. In an alternative format, the probe(s) are immobilizedon a solid surface and the mRNA is contacted with the probe(s), forexample, in an Affymetrix gene chip array. A skilled artisan can readilyadapt known mRNA detection methods for use in detecting the level ofmRNA encoded by the markers of the present invention.

An alternative method for determining the level of mRNA marker in asample involves the process of nucleic acid amplification, e.g., byrtPCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat.No. 4,683,202), ligase chain reaction (Barany, 1991, Proc. Natl. Acad.Sci. USA, 88:189-193), self sustained sequence replication (Guatelli etal., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptionalamplification system (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA86:1173-1177), Q-Beta Replicase (Lizardi et al., 1988, Bio/Technology6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No.5,854,033) or any other nucleic acid amplification method, followed bythe detection of the amplified molecules using techniques well known tothose of skill in the art. These detection schemes are especially usefulfor the detection of nucleic acid molecules if such molecules arepresent in very low numbers. As used herein, amplification primers aredefined as being a pair of nucleic acid molecules that can anneal to 5′or 3′ regions of a gene (plus and minus strands, respectively, orvice-versa) and contain a short region in between. In general,amplification primers are from about 10 to 30 nucleotides in length andflank a region from about 50 to 200 nucleotides in length. Underappropriate conditions and with appropriate reagents, such primerspermit the amplification of a nucleic acid molecule comprising thenucleotide sequence flanked by the primers.

For in situ methods, mRNA does not need to be isolated from the breastcells prior to detection. In such methods, a cell or tissue sample isprepared/processed using known histological methods. The sample is thenimmobilized on a support, typically a glass slide, and then contactedwith a probe that can hybridize to mRNA that encodes the marker.

As an alternative to making determinations based on the absoluteexpression level of the marker, determinations may be based on thenormalized expression level of the marker. Expression levels arenormalized by correcting the absolute expression level of a marker bycomparing its expression to the expression of a gene that is not amarker, e.g., a housekeeping gene that is constitutively expressed.Suitable genes for normalization include housekeeping genes such as theactin gene, or epithelial cell-specific genes. This normalization allowsthe comparison of the expression level in one sample, e.g., a patientsample, to another sample, e.g., a non-breast cancer sample, or betweensamples from different sources.

Alternatively, the expression level can be provided as a relativeexpression level. To determine a relative expression level of a marker,the level of expression of the marker is determined for 10 or moresamples of normal versus cancer cell isolates, preferably 50 or moresamples, prior to the determination of the expression level for thesample in question. The mean expression level of each of the genesassayed in the larger number of samples is determined and this is usedas a baseline expression level for the marker. The expression level ofthe marker determined for the test sample (absolute level of expression)is then divided by the mean expression value obtained for that marker.This provides a relative expression level.

Preferably, the samples used in the baseline determination will be frombreast cancer or from non-breast cancer cells of breast tissue. Thechoice of the cell source is dependent on the use of the relativeexpression level. Using expression found in normal tissues as a meanexpression score aids in validating whether the marker assayed is breastspecific (versus normal cells). In addition, as more data isaccumulated, the mean expression value can be revised, providingimproved relative expression values based on accumulated data.Expression data from breast cells provides a means for grading theseverity of the breast cancer state.

In another embodiment of the present invention, a marker protein isdetected. A preferred agent for detecting marker protein of theinvention is an antibody capable of binding to such a protein or afragment thereof, preferably an antibody with a detectable label.Antibodies can be polyclonal, or more preferably, monoclonal. An intactantibody, or a fragment or derivative thereof (e.g., Fab or F(ab′)₂) canbe used. The term “labeled”, with regard to the probe or antibody, isintended to encompass direct labeling of the probe or antibody bycoupling (i.e., physically linking) a detectable substance to the probeor antibody, as well as indirect labeling of the probe or antibody byreactivity with another reagent that is directly labeled. Examples ofindirect labeling include detection of a primary antibody using afluorescently labeled secondary antibody and end-labeling of a DNA probewith biotin such that it can be detected with fluorescently labeledstreptavidin.

Proteins from breast cells can be isolated using techniques that arewell known to those of skill in the art. The protein isolation methodsemployed can, for example, be such as those described in Harlow and Lane(Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y.).

A variety of formats can be employed to determine whether a samplecontains a protein that binds to a given antibody. Examples of suchformats include, but are not limited to, enzyme immunoassay (EIA),radioimmunoassay (RIA), Western blot analysis and enzyme linkedimmunoabsorbant assay (ELISA). A skilled artisan can readily adapt knownprotein/antibody detection methods for use in determining whether breastcells express a marker of the present invention.

In one format, antibodies, or antibody fragments or derivatives, can beused in methods such as Western blots or immunofluorescence techniquesto detect the expressed proteins. In such uses, it is generallypreferable to immobilize either the antibody or proteins on a solidsupport. Suitable solid phase supports or carriers include any supportcapable of binding an antigen or an antibody. Well-known supports orcarriers include glass, polystyrene, polypropylene, polyethylene,dextran, nylon, amylases, natural and modified celluloses,polyacrylamides, gabbros, and magnetite.

One skilled in the art will know many other suitable carriers forbinding antibody or antigen, and will be able to adapt such support foruse with the present invention. For example, protein isolated frombreast cells can be run on a polyacrylamide gel electrophoresis andimmobilized onto a solid phase support such as nitrocellulose. Thesupport can then be washed with suitable buffers followed by treatmentwith the detectably labeled antibody. The solid phase support can thenbe washed with the buffer a second time to remove unbound antibody. Theamount of bound label on the solid support can then be detected byconventional means.

The invention also encompasses kits for detecting the presence of amarker protein or nucleic acid in a biological sample (e.g. abreast-associated body fluid such as a nipple aspirate). Such kits canbe used to determine if a subject is suffering from or is at increasedrisk of developing breast cancer. For example, the kit can comprise alabeled compound or agent capable of detecting a marker protein ornucleic acid in a biological sample and means for determining the amountof the protein or mRNA in the sample (e.g., an antibody which binds theprotein or a fragment thereof, or an oligonucleotide probe which bindsto DNA or mRNA encoding the protein). Kits can also include instructionsfor interpreting the results obtained using the kit.

For antibody-based kits, the kit can comprise, for example: (1) a firstantibody (e.g., attached to a solid support) which binds to a markerprotein; and, optionally, (2) a second, different antibody which bindsto either the protein or the first antibody and is conjugated to adetectable label.

For oligonucleotide-based kits, the kit can comprise, for example: (1)an oligonucleotide, e.g., a detectably labeled oligonucleotide, whichhybridizes to a nucleic acid sequence encoding a marker protein or (2) apair of primers useful for amplifying a marker nucleic acid molecule.The kit can also comprise, e.g., a buffering agent, a preservative, or aprotein stabilizing agent. The kit can further comprise componentsnecessary for detecting the detectable label (e.g., an enzyme or asubstrate). The kit can also contain a control sample or a series ofcontrol samples which can be assayed and compared to the test sample.Each component of the kit can be enclosed within an individual containerand all of the various containers can be within a single package, alongwith instructions for interpreting the results of the assays performedusing the kit.

B. Pharmacogenomics

The markers of the invention are also useful as pharmacogenomic markers.As used herein, a “pharmacogenomic marker” is an objective biochemicalmarker whose expression level correlates with a specific clinical drugresponse or susceptibility in a patient (see, e.g., McLeod et al. (1999)Eur. J. Cancer 35(12): 1650-1652). The presence or quantity of thepharmacogenomic marker expression is related to the predicted responsiveof the patient and more particularly the patient's tumor to therapy witha specific drug or class of drugs. By assessing the presence or quantityof the expression of one or more pharmacogenomic markers in a patient, adrug therapy which is most appropriate for the patient, or which ispredicted to have a greater degree of success, may be selected. Forexample, based on the presence or quantity of RNA or protein encoded byspecific tumor markers in a patient, a drug or course of treatment maybe selected that is optimized for the treatment of the specific tumorlikely to be present in the patient. The use of pharmacogenomic markerstherefore permits selecting or designing the most appropriate treatmentfor each cancer patient without trying different drugs or regimes.

Another aspect of pharmacogenomics deals with genetic conditions thatalters the way the body acts on drugs. These pharmacogenetic conditionscan occur either as rare defects or as polymorphisms. For example,glucose-6-phosphate dehydrogenase (G6PD) deficiency is a commoninherited enzymopathy in which the main clinical complication ishemolysis after ingestion of oxidant drugs (anti-malarials,sulfonamides, analgesics, nitrofurans) and consumption of fava beans.

As an illustrative embodiment, the activity of drug metabolizing enzymesis a major determinant of both the intensity and duration of drugaction. The discovery of genetic polymorphisms of drug metabolizingenzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymesCYP2D6 and CYP2C19) has provided an explanation as to why some patientsdo not obtain the expected drug effects or show exaggerated drugresponse and serious toxicity after taking the standard and safe dose ofa drug. These polymorphisms are expressed in two phenotypes in thepopulation, the extensive metabolizer (EM) and poor metabolizer (PM).The prevalence of PM is different among different populations. Forexample, the gene coding for CYP2D6 is highly polymorphic and severalmutations have been identified in PM, which all lead to the absence offunctional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quitefrequently experience exaggerated drug response and side effects whenthey receive standard doses. If a metabolite is the active therapeuticmoiety, a PM will show no therapeutic response, as demonstrated for theanalgesic effect of codeine mediated by its CYP2D6-formed metabolitemorphine. The other extreme are the so called ultra-rapid metabolizerswho do not respond to standard doses. Recently, the molecular basis ofultra-rapid metabolism has been identified to be due to CYP2D6 geneamplification.

Thus, the level of expression of a marker of the invention in anindividual can be determined to thereby select appropriate agent(s) fortherapeutic or prophylactic treatment of the individual. In addition,pharmacogenetic studies can be used to apply genotyping of polymorphicalleles encoding drug-metabolizing enzymes to the identification of anindividual's drug responsiveness phenotype. This knowledge, when appliedto dosing or drug selection, can avoid adverse reactions or therapeuticfailure and thus enhance therapeutic or prophylactic efficiency whentreating a subject with a modulator of expression of a marker of theinvention.

C. Monitoring Clinical Trials

Monitoring the influence of agents (e.g., drug compounds) on the levelof expression of a marker of the invention can be applied not only inbasic drug screening, but also in clinical trials. For example, theeffectiveness of an agent to affect marker expression can be monitoredin clinical trials of subjects receiving treatment for breast cancer. Ina preferred embodiment, the present invention provides a method formonitoring the effectiveness of treatment of a subject with an agent(e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleicacid, small molecule, or other drug candidate) comprising the steps of(i) obtaining a pre-administration sample from a subject prior toadministration of the agent; (ii) detecting the level of expression ofone or more selected markers of the invention in the pre-administrationsample; (iii) obtaining one or more post-administration samples from thesubject; (iv) detecting the level of expression of the marker(s) in thepost-administration samples; (v) comparing the level of expression ofthe marker(s) in the pre-administration sample with the level ofexpression of the marker(s) in the post-administration sample orsamples; and (vi) altering the administration of the agent to thesubject accordingly. For example, increased expression of marker gene(s)during the course of treatment may indicate ineffective dosage and thedesirability of increasing the dosage. Conversely, decreased expressionof the marker gene(s) may indicate efficacious treatment and no need tochange dosage.

D. Electronic Apparatus Readable Media and Arrays

Electronic apparatus readable media comprising a marker of the presentinvention is also provided. As used herein, “electronic apparatusreadable media” refers to any suitable medium for storing, holding orcontaining data or information that can be read and accessed directly byan electronic apparatus. Such media can include, but are not limited to:magnetic storage media, such as floppy discs, hard disc storage medium,and magnetic tape; optical storage media such as compact disc;electronic storage media such as RAM, ROM, EPROM, EEPROM and the like;general hard disks and hybrids of these categories such asmagnetic/optical storage media. The medium is adapted or configured forhaving recorded thereon a marker of the present invention.

As used herein, the term “electronic apparatus” is intended to includeany suitable computing or processing apparatus or other deviceconfigured or adapted for storing data or information. Examples ofelectronic apparatus suitable for use with the present invention includestand-alone computing apparatus; networks, including a local areanetwork (LAN), a wide area network (WAN) Internet, Intranet, andExtranet; electronic appliances such as a personal digital assistants(PDAs), cellular phone, pager and the like; and local and distributedprocessing systems.

As used herein, “recorded” refers to a process for storing or encodinginformation on the electronic apparatus readable medium. Those skilledin the art can readily adopt any of the presently known methods forrecording information on known media to generate manufactures comprisingthe markers of the present invention.

A variety of software programs and formats can be used to store themarker information of the present invention on the electronic apparatusreadable medium. For example, the marker nucleic acid sequence can berepresented in a word processing text file, formatted incommercially-available software such as WordPerfect and MicroSoft Word,or represented in the form of an ASCII file, stored in a databaseapplication, such as DB2, Sybase, Oracle, or the like, as well as inother forms. Any number of data processor structuring formats (e.g.,text file or database) may be employed in order to obtain or create amedium having recorded thereon the markers of the present invention.

By providing the markers of the invention in readable form, one canroutinely access the marker sequence information for a variety ofpurposes. For example, one skilled in the art can use the nucleotide oramino acid sequences of the present invention in readable form tocompare a target sequence or target structural motif with the sequenceinformation stored within the data storage means. Search means are usedto identify fragments or regions of the sequences of the invention whichmatch a particular target sequence or target motif.

The present invention therefore provides a medium for holdinginstructions for performing a method for determining whether a subjecthas breast cancer or a pre-disposition to breast cancer, wherein themethod comprises the steps of determining the presence or absence of amarker and based on the presence or absence of the marker, determiningwhether the subject has breast cancer or a pre-disposition to breastcancer and/or recommending a particular treatment for breast cancer orpre-breast cancer condition.

The present invention further provides in an electronic system and/or ina network, a method for determining whether a subject has breast canceror a pre-disposition to breast cancer associated with a marker whereinthe method comprises the steps of determining the presence or absence ofthe marker, and based on the presence or absence of the marker,determining whether the subject has breast cancer or a pre-dispositionto breast cancer, and/or recommending a particular treatment for thebreast cancer or pre-breast cancer condition. The method may furthercomprise the step of receiving phenotypic information associated withthe subject and/or acquiring from a network phenotypic informationassociated with the subject.

The present invention also provides in a network, a method fordetermining whether a subject has breast cancer or a pre-disposition tobreast cancer associated with a marker, said method comprising the stepsof receiving information associated with the marker receiving phenotypicinformation associated with the subject, acquiring information from thenetwork corresponding to the marker and/or breast cancer, and based onone or more of the phenotypic information, the marker, and the acquiredinformation, determining whether the subject has a breast cancer or apre-disposition to breast cancer. The method may further comprise thestep of recommending a particular treatment for the breast cancer orpre-breast cancer condition.

The present invention also provides a business method for determiningwhether a subject has breast cancer or a pre-disposition to breastcancer, said method comprising the steps of receiving informationassociated with the marker, receiving phenotypic information associatedwith the subject, acquiring information from the network correspondingto the marker and/or breast cancer, and based on one or more of thephenotypic information, the marker, and the acquired information,determining whether the subject has breast cancer or a pre-dispositionto breast cancer. The method may further comprise the step ofrecommending a particular treatment for the breast cancer or pre-breastcancer condition.

The invention also includes an array comprising a marker of the presentinvention. The array can be used to assay expression of one or moregenes in the array. In one embodiment, the array can be used to assaygene expression in a tissue to ascertain tissue specificity of genes inthe array. In this manner, up to about 7600 genes can be simultaneouslyassayed for expression. This allows a profile to be developed showing abattery of genes specifically expressed in one or more tissues.

In addition to such qualitative determination, the invention allows thequantitation of gene expression. Thus, not only tissue specificity, butalso the level of expression of a battery of genes in the tissue isascertainable. Thus, genes can be grouped on the basis of their tissueexpression per se and level of expression in that tissue. This isuseful, for example, in ascertaining the relationship of gene expressionbetween or among tissues. Thus, one tissue can be perturbed and theeffect on gene expression in a second tissue can be determined. In thiscontext, the effect of one cell type on another cell type in response toa biological stimulus can be determined. Such a determination is useful,for example, to know the effect of cell-cell interaction at the level ofgene expression. If an agent is administered therapeutically to treatone cell type but has an undesirable effect on another cell type, theinvention provides an assay to determine the molecular basis of theundesirable effect and thus provides the opportunity to co-administer acounteracting agent or otherwise treat the undesired effect. Similarly,even within a single cell type, undesirable biological effects can bedetermined at the molecular level. Thus, the effects of an agent onexpression of other than the target gene can be ascertained andcounteracted.

In another embodiment, the array can be used to monitor the time courseof expression of one or more genes in the array. This can occur invarious biological contexts, as disclosed herein, for exampledevelopment of breast cancer, progression of breast cancer, andprocesses, such a cellular transformation associated with breast cancer.

The array is also useful for ascertaining the effect of the expressionof a gene on the expression of other genes in the same cell or indifferent cells. This provides, for example, for a selection ofalternate molecular targets for therapeutic intervention if the ultimateor downstream target cannot be regulated.

The array is also useful for ascertaining differential expressionpatterns of one or more genes in normal and abnormal cells. Thisprovides a battery of genes that could serve as a molecular target fordiagnosis or therapeutic intervention.

E. Surrogate Markers

The markers of the invention may serve as surrogate markers for one ormore disorders or disease states or for conditions leading up to diseasestates, and in particular, breast cancer. As used herein, a “surrogatemarker” is an objective biochemical marker which correlates with theabsence or presence of a disease or disorder, or with the progression ofa disease or disorder (e.g., with the presence or absence of a tumor).The presence or quantity of such markers is independent of the disease.Therefore, these markers may serve to indicate whether a particularcourse of treatment is effective in lessening a disease state ordisorder. Surrogate markers are of particular use when the presence orextent of a disease state or disorder is difficult to assess throughstandard methodologies (e.g., early stage tumors), or when an assessmentof disease progression is desired before a potentially dangerousclinical endpoint is reached (e.g., an assessment of cardiovasculardisease may be made using cholesterol levels as a surrogate marker, andan analysis of HIV infection may be made using HIV RNA levels as asurrogate marker, well in advance of the undesirable clinical outcomesof myocardial infarction or fully-developed AIDS). Examples of the useof surrogate markers in the art include: Koomen et al. (2000) J. Mass.Spectrom. 35: 258-264; and James (1994) AIDS Treatment News Archive 209.

The markers of the invention are also useful as pharmacodynamic markers.As used herein, a “pharmacodynamic marker” is an objective biochemicalmarker which correlates specifically with drug effects. The presence orquantity of a pharmacodynamic marker is not related to the disease stateor disorder for which the drug is being administered; therefore, thepresence or quantity of the marker is indicative of the presence oractivity of the drug in a subject. For example, a pharmacodynamic markermay be indicative of the concentration of the drug in a biologicaltissue, in that the marker is either expressed or transcribed or notexpressed or transcribed in that tissue in relationship to the level ofthe drug. In this fashion, the distribution or uptake of the drug may bemonitored by the pharmacodynamic marker. Similarly, the presence orquantity of the pharmacodynamic marker may be related to the presence orquantity of the metabolic product of a drug, such that the presence orquantity of the marker is indicative of the relative breakdown rate ofthe drug in vivo. Pharmacodynamic markers are of particular use inincreasing the sensitivity of detection of drug effects, particularlywhen the drug is administered in low doses. Since even a small amount ofa drug may be sufficient to activate multiple rounds of markertranscription or expression, the amplified marker may be in a quantitywhich is more readily detectable than the drug itself. Also, the markermay be more easily detected due to the nature of the marker itself; forexample, using the methods described herein, antibodies may be employedin an immune-based detection system for a protein marker, ormarker-specific radiolabeled probes may be used to detect a mRNA marker.Furthermore, the use of a pharmacodynamic marker may offermechanism-based prediction of risk due to drug treatment beyond therange of possible direct observations. Examples of the use ofpharmacodynamic markers in the art include: Matsuda et al. U.S. Pat. No.6,033,862; Hattis et al. (1991) Env. Health Perspect. 90: 229-238;Schentag (1999) Am. J. Health-Syst. Pharm. 56 Suppl. 3: S21-S24; andNicolau (1999) Am, J. Health-Syst. Pharm. 56 Suppl. 3: S16-S20.

VI. Experimental Protocol

A. Identification of Markers and Assembly of their Sequence

Subtracted libraries were generated using a PCR based method thatproduced cDNAs of mRNAs that are present at a higher level in one mRNApopulation (the tester) as compared to a second mRNA population (thedriver). Both tester and driver mRNA populations were converted intocDNA by reverse transcription, and then PCR amplified using the SMARTPCR kit from Clontech. Tester and driver cDNAs were then hybridizedusing the PCR-Select cDNA subtraction kit from Clontech. This techniqueeffected both a subtraction and normalization of the cDNA. Normalizationapproximately equalizes the copy numbers of low-abundance andhigh-abundance cDNA species. After generation of the subtractedlibraries from the subtracted and normalized cDNA, 96 or more cDNAclones from each subtracted library were tested to confirm differentialexpression by reverse Southern hybridization.

Various subtracted libraries were constructed to isolate cDNA clones ofdifferent breast cancer marker genes. For isolating cDNA clones of genesexpressed at high levels in aggressive or metastatic breast tumors, thesubtracted libraries were constructed using tester cDNA generated frombreast tumor tissues of patients having poor clinical outcome oraggressive tumors, or from cell lines derived from aggressive breasttumors, and driver cDNA generated from breast tumor tissues of patientshaving good clinical outcome or indolent tumors, or from cell linesderived from indolent breast tumors. “Poor clinical outcome” is asituation where the patient suffered cancer relapse within three yearsfollowing breast cancer surgery. “Good clinical outcome” is a situationwhere the patient remained cancer free for over five years followingbreast cancer surgery. For isolating cDNA clones of genes expressed athigh levels in non-aggressive or indolent breast tumors, the subtractedlibraries were constructed using tester cDNA generated from breast tumortissues of patients having good clinical outcome or indolent tumors, orfrom cell lines derived from indolent breast tumors, and driver cDNAgenerated from breast tumor tissues of patients having poor clinicaloutcome or having aggressive breast tumors, or from cell lines derivedfrom aggressive breast tumors. Markers 405 and 411 were identified usingsuch subtracted libraries.

Table 1 lists all of the markers of the invention. The markers listed inTable 2 were identified by transcription profiling using mRNA from 23IDC node negative breast tumors with good outcome, defined as greaterthan five years of disease-free survival, and 16 IDC node negativebreast tumors with poor clinical outcome, defined as less than threeyears of disease free survival. Clones having expression of at leastthree-fold higher in at least 25% of poor clinical outcome tumorscompared to their expression in node negative, good clinical outcometumors were designated as poor clinical outcome tumor specific markers.These cDNA clones were selected to have their protein-encodingtranscript sequences determined.

The markers listed in Table 3 were identified by transcription profilingusing mRNA from 16 IDC node negative breast tumors and 19 IDC nodepositive breast tumors. Clones having expression of at least five-foldhigher in at least 15% of node-positive tumors, as compared to theirexpression in node negative tumors, were designated as node-positivetumor specific markers. These cDNA clones were selected to have theirprotein-encoding transcript sequences determined.

The markers of Table 4 were identified by transcription profiling usingmRNA from 25 IDC node negative breast tumors with good outcome, definedas greater than five years of disease-free survival, and 18 IDC nodenegative breast tumors with poor clinical outcome, defined as less thanthree years of disease free survival. Clones having expression of atleast five-fold higher in at least 15% of poor clinical outcome tumorscompared to their expression in node negative, good clinical outcometumors were designated as poor clinical outcome tumor specific markers.These cDNA clones were selected to have their protein-encodingtranscript sequences determined.

In order to determine the full-length protein-encoding transcripts forthe selected cDNA clones, the clusters in which the selected clonesbelong were blasted against both public and proprietary sequencedatabases in order to identify other EST sequences or clusters withsignificant overlap. Thus, contiguous EST sequences and/or clusters wereassembled into protein-encoding transcripts.

An identification of protein sequence within each transcript wasaccomplished by obtaining one of the following:

-   -   a) a direct match between the protein sequence and at least one        EST sequence in one of its 6 possible translations;    -   b) a direct match between the nucleotide sequence for the mRNA        corresponding to the protein sequence and at least one EST        sequence;    -   c) a match between the protein sequence and a contiguous        assembly (contig) of the EST sequences with other available EST        sequences in the databases in one of its 6 possible        translations; or    -   d) a match between the nucleotide sequence for the mRNA        corresponding to the protein sequence and a contiguous assembly        of the EST sequences with other available EST sequences in the        databases in one of its 6 possible translations.

Markers M422, M254 and M421 are very similar (>90%) and can be mapped toan overlapping region on chromosome 22. Marker M421 is identical to theprobe sequence on the transcriptional profiling array. Each transcriptcan be distinguished from the others based on the PCR products generatedfrom unique primer pairs. With breast tumor RNA as the template, onlythe Marker M421 product was observed. The PCR expression profilecorrelated very well with the transcriptional profiling data.

The expression of several node-positive tumor specific clones werefurther examined by in situ hybridization (ISH) experiments using atissue microarray containing 23 node negative IDC breast tumors and 26node-positive IDC paraffin-embedded tumor samples. Table 12 listsmarkers which showed increased expression in node-positive IDCs, ascompared to node-negative IDCs, as determined by in situ hybridization.

B. Summary of the Data

Tables 1-12 list markers of the invention obtained using the foregoingexperimental protocol. The Tables provide the name of the genecorresponding to the marker (“Gene Name”), the sequence listingidentifier of the cDNA sequence of a nucleotide transcript encoded by orcorresponding to the marker (“SEQ ID NO (nts)”), the sequence listingidentifier of the amino acid sequence of a protein encoded by thenucleotide transcript (“SEQ ID NO (AAs)”), and the location of theprotein coding sequence within the cDNA sequence (“CDS”).

Table 1 lists all of the markers of the invention, which areover-expressed in breast cancer cells compared to normal (i.e.,non-cancerous) breast cells. Table 2 lists markers identified bytranscription profiling using mRNA from 23 IDC node negative breasttumors with good outcome and 16 IDC node negative breast tumors withpoor clinical outcome. Table 3 lists markers identified by transcriptionprofiling using mRNA from 16 IDC node negative breast tumors and 19 IDCnode positive breast tumors. Table 4 lists markers identified bytranscription profiling using mRNA from 25 IDC node negative breasttumors with good outcome and 18 IDC node negative breast tumors withpoor clinical outcome. Table 5 lists markers particularly useful inscreening for the presence of breast cancer (“screening markers”). Table6 lists markers particularly useful in assessing aggressiveness ofbreast cancer (“aggressiveness markers”). Table 7 lists markersparticularly useful for both screening breast cancer and assessingaggressiveness of breast cancer. Table 8 lists markers whoseover-expression correlates with good clinical outcome, i.e., greaterthan 5 years of disease-free survival. Table 9 lists markers whoseover-expression correlates with poor clinical outcome, i.e., less than 3years of disease-free survival. Table 10 lists newly identified nucleicacid and amino acid sequences. Table 11 lists newly identified nucleicacid sequences. Table 12 lists staging markers whose expressioncorrelates with metastasis to lymph nodes.

The contents of all references, patents, published patent applications,and database records including GenBank, IMAGE consortium and Derwentcited throughout this application, are hereby incorporated by reference.

Other Embodiments

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims:

TABLE 1 SEQ ID SEQ ID NO NO Marker Gene Name (nts) (AAs) CDS M552 AEBP1:AE-binding protein 1 1 2 140 . . . 3616 M83 AKR1C1: aldo-keto reductasefamily 1, member C1 3 4  7 . . . 978 (20-alpha (3-alpha)-hydroxysteroiddehydrogenase) M84 AKR1C3: aldo-keto reductase family 1, member C3 5 6 1 . . . 972 (3-alpha hydroxysteroid dehydrogenase, type II) M85 ALDOB:aldolase B, fructose-bisphosphate 7 8 126 . . . 1220 M86 AQP3: Aquaporin3, variant 1 9 10 65 . . . 943 M87 AQP3: Aquaporin 3, variant 2 11 10 65. . . 943 M88 AREG: amphiregulin (schwannoma-derived growth 12 13 210 .. . 968  factor) M391 ARHGEF12: Rho guanine exchange factor (GEF) 12 1415  8 . . . 4642 M672 ASS: argininosuccinate synthetase, transcript 1617  76 . . . 1314 variant 1 M673 ASS: argininosuccinate synthetase,transcript 18 19  81 . . . 1319 variant 2 M200 ATP5A1: ATP synthase, H+transporting, 20 21  59 . . . 1720 mitochondrial F1 complex, alphasubunit, isoform 1, cardiac muscle M366 AZGP1: alpha-2-glycoprotein 1,zinc 22 23  1 . . . 897 M392 BAK1: BCL2-antagonist/killer 1 24 25 201 .. . 836  M89 BF: B-factor, properdin 26 27  41 . . . 2335 M201 BGN:biglycan 28 29 121 . . . 1227 M90 BMI1: murine leukemia viral (bmi-1)oncogene 30 31 480 . . . 1460 homolog M394 C1orf21: chromosome 1 openreading frame 21 32 33 400 . . . 765  M202 CALM1: calmodulin 1(phosphorylase kinase, delta) 34 35 200 . . . 649  M92 CART: cocaine-and amphetamine-regulated 36 37 20 . . . 370 transcript M367 CD24: CD24antigen (small cell lung carcinoma 38 39 57 . . . 299 cluster 4 antigen)M95 CDC2: cell division cycle 2, G1 to S and G2 to M 40 41 127 . . .1020 M203 CDH2: cadherin 2, type 1, N-cadherin (neuronal) 42 43 102 . .. 2822 M96 CEGP1: CEGP1 protein 44 45  81 . . . 3080 M97 CEZANNE: zincfinger protein Cezanne 46 47 155 . . . 2731 M98 CGI-52: CGI-52 protein,similar to 48 49 277 . . . 1356 phosphatidylcholine transfer protein 2M99 CGI-72: CGI-72 protein 50 51  70 . . . 1401 M254 CGI-96: CGI-96protein 52 53 175 . . . 1146 M100 CLECSF1: C-type (calcium dependent, 5455 80 . . . 673 carbohydrate-recognition domain) lectin, superfamilymember 1 (cartilage-derived), variant 1 M553 CLECSF1: C-type (calciumdependent, 56 57 53 . . . 673 carbohydrate-recognition domain) lectin,superfamily member 1 (cartilage-derived), variant 2 M204 COL10A1:collagen, type X, alpha 1 (Schmid 58 59  1 . . . 2043 metaphysealchondrodysplasia) M205 COL12A1: collagen, type XII, alpha 1, variant 160 61  1 . . . 9192 M618 COL12A1: collagen, type XII, alpha 1, variant 262 63 114 . . . 9305 M12 COL1A1: collagen, type I, alpha 1, variant 1 6465 120 . . . 4514 M494 COL1A1: collagen, type I, alpha 1, variant 2 6665 120 . . . 4514 M206 COL3A1: collagen, type III, alpha 1(Ehlers-Danlos 67 68 103 . . . 4503 syndrome type IV, autosomaldominant) M101 COL5A2: collagen, type V, alpha 2 69 70 139 . . . 4629M102 COMP: cartilage oligomeric matrix protein 71 72  26 . . . 2299(pseudoachondroplasia, epiphyseal dysplasia 1, multiple) M207 COX6C:cytochrome c oxidase subunit VIc 73 74 68 . . . 295 OV7 CP:ceruloplasmin (ferroxidase), variant 1 75 76  <1 . . . 2561 OV8 CP:ceruloplasmin (ferroxidase), variant 2 77 78  1 . . . 3198 OV66 CP:ceruloplasmin (ferroxidase), variant 3 79 80  1 . . . 3210 M103 CRABP2:cellular retinoic acid-binding protein 2 81 82 138 . . . 554  M16 CRIP1:cysteine-rich protein 1 (intestinal) 83 84  1 . . . 234 M104 CrkRS:CDC2-related protein kinase 7 85 86  34 . . . 4506 M395 CSK: c-srctyrosine kinase 87 88 413 . . . 1765 M105 CSPG2: chondroitin sulfateproteoglycan 2 89 90 267 . . . 7496 (versican) M208 CTBP2: C-terminalbinding protein 2, isoform 1 91 92 346 . . . 1683 M209 CTBP2: C-terminalbinding protein 2, isoform 2 93 94 137 . . . 3094 M396 CYP1B1:cytochrome P450, subfamily I (dioxin- 95 96 373 . . . 2004 inducible),polypeptide 1 M106 CYP24: cytochrome P450, subfamily XXIV (vitamin 97 98405 . . . 1946 D 24-hydroxylase) OV40 DD96: Epithelial proteinup-regulated in carcinoma, 99 100 202 . . . 546  membrane associatedprotein 17 M142 DEME-6: DEME-6 protein 101 102  <1 . . . 1725 M107DJ167A19: hypothetical protein DJ167A19.1 103 104  1 . . . 921 M108DKFZP564D166: putative ankyrin-repeat containing 105 106  95 . . . 3400protein M109 DKFZP564D206: hypothetical protein 107 108 <1 . . . 405DKFZP564D206 M82 DKFZp564I1922: adlican 109 110  1 . . . 8487 M110DKFZP566I133: hypothetical protein 111 112 134 . . . 1354 DKFZp566I133,variant 1 M554 DKFZP566I133: hypothetical protein 113 114 134 . . . 1354DKFZp566I133, variant 2 M111 DNAJL1: hypothetical protein similar tomouse 115 116 203 . . . 1225 Dnajl1 M112 DRIL1: dead ringer(Drosophila)-like 1 117 118 201 . . . 1982 M555 DUSP4: dual specificityphosphatase 4 119 120 502 . . . 1686 M210 EDIL3: EGF-like repeats anddiscoidin I-like 121 122 111 . . . 1553 domains 3 M211 ENO1: enolase 1,(alpha) 123 124  95 . . . 1399 M113 ERBB2: v-erb-b2 avian erythroblasticleukemia viral 125 126 151 . . . 3919 oncogene homolog 2(neuro/glioblastoma derived oncogene homolog) M114 ESR1: estrogenreceptor 1 127 128 361 . . . 2148 M115 F2R: coagulation factor II(thrombin) receptor 129 130 345 . . . 1622 M116 FABP7: B-FABP, fattyacid binding protein 7 131 132 77 . . . 475 M117 FACL2:fatty-acid-Coenzyme A ligase, long-chain 2 133 134  14 . . . 2110 M118FAP: fibroblast activation protein, alpha 135 136 209 . . . 2491 M397FGF7: fibroblast growth factor 7 (keratinocyte growth 137 138 446 . . .1030 factor) M119 FKBP4: FK506-binding protein 4 139 140 100 . . . 1479M212 FKSG12: pancreas tumor-related protein 141 142 238 . . . 1125 M120FLJ12425: hypothetical protein FLJ12425 143 144 42 . . . 335 M121FLJ12910: hypothetical protein FLJ12910 145 146 260 . . . 1585 M122FLJ13187: hypothetical protein FLJ13187 147 148 98 . . . 847 M123FLJ14103: hypothetical protein FLJ14103 149 150 76 . . . 624 M398FLJ20171: hypothetical protein FLJ20171 151 152  58 . . . 1134 M514FLJ20940: hypothetical protein FLJ20940 153 154 236 . . . 742  M399FLJ21174: hypothetical protein FLJ21174 155 156 234 . . . 881  M124FLJ21213: hypothetical protein FLJ21213 157 158  3 . . . 809 M125FLJ21879: hypothetical protein FLJ21879 159 160  75 . . . 1043 M126FLJ22002: hypothetical protein FLJ22002 161 162 116 . . . 784  M400FLJ22418: hypothetical protein FLJ22418 163 164 71 . . . 919 M213 FXYD3:FXYD domain-containing ion transport 165 166 176 . . . 439  regulator 3,isoform 1 M214 FXYD3: FXYD domain-containing ion transport 167 168 260 .. . 601  regulator 3, isoform 2 M127 G1P3: interferon, alpha-inducibleprotein (clone IFI- 169 170 108 . . . 500  6-16) M215 GABRP:gamma-aminobutyric acid (GABA) A 171 172 157 . . . 1479 receptor, piM128 GATA2: GATA-binding protein 2 173 174 194 . . . 1618 M216 GATA3:GATA-binding protein 3, variant 1 175 176 461 . . . 1792 M217 GATA3:GATA-binding protein 3, variant 2 177 176 461 . . . 1792 M218 GATA3:GATA-binding protein 3, variant 3 178 176 152 . . . 1483 M129 GNLY:granulysin, isoform 519 179 180 281 . . . 670  M130 GNLY: granulysin,isoform NKG5 181 182 129 . . . 566  M271 GOLPH2: golgi phosphoprotein 2183 184 151 . . . 1353 M219 GPD2: glycerol-3-phosphate dehydrogenase 2185 186 124 . . . 2307 (mitochondrial) M131 GPI: glucose phosphateisomerase 187 188  16 . . . 1692 M132 GRIA2: glutamate receptor,ionotropic, AMPA 2 189 190 161 . . . 2812 M495 GSTP1: glutathioneS-transferase pi 191 192 30 . . . 662 M220 GUCY1A3: guanylate cyclase 1,soluble, alpha 3, 193 194 520 . . . 2592 variant 1 M221 GUCY1A3:guanylate cyclase 1, soluble, alpha 3, 195 194 386 . . . 2458 variant 2M222 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 196 194 407 . . .2479 variant 3 M133 GZMA: Granzyme A (Cytotoxic T-lymphocyte- 197 198 39. . . 827 associated serine esterase-3; Hanukah factor serine protease);CTL tryptase M199 HAG-2: anterior gradient 2 (Xenopus laevis) 199 200 59. . . 586 homolog M196 HAG-3: anterior gradient protein 3, variant 1 201202 49 . . . 549 M225 HAG-3: anterior gradient protein 3, variant 2 203204 116 . . . 129  M134 HDAC2: histone deacetylase 2 205 206 205 . . .1671 M273 HMGCS2: 3-hydroxy-3-methylglutaryl-Coenzyme A 207 208  52 . .. 1578 synthase 2 (mitochondrial) M674 HN1: hematological andneurological expressed 1 209 210 104 . . . 568  M223 HNF3A: hepatocytenuclear factor 3, alpha 211 212  88 . . . 1509 M135 HOXB2: homeo box B2213 214  79 . . . 1149 M136 HPD: 4-hydroxyphenylpyruvate dioxygenase 215216  26 . . . 1207 M137 HPGD: hydroxyprostaglandin dehydrogenase 15- 217218 18 . . . 818 (NAD) M401 HSCP1: serine carboxypeptidase 1 precursor219 220  33 . . . 1391 protein M224 HSPC155: hypothetical proteinHSPC155 221 222 241 . . . 744  M402 HSPD1: heat shock 60 kD protein 1(chaperonin) 223 224  25 . . . 1746 M403 IGF1R: insulin-like growthfactor 1 receptor 225 226  46 . . . 4149 M139 IGSF1: IGCD1, IGDC1,KIAA036, immunoglobulin 227 228  81 . . . 4091 superfamily, member 1M404 IL6ST: interleukin 6 signal transducer (gp130, 229 230 256 . . .3012 oncostatin M receptor) M34 INHBA: Inhibin, beta-1 (activin A,activin AB alpha 231 232  86 . . . 1366 polypeptide) M140 ISG15:interferon-stimulated protein, 15 kDa 233 234 76 . . . 573 M226 JCL-1:hepatocellular carcinoma associated protein; 235 236  70 . . . 1890breast cancer associated gene 1 M556 JUN: v-jun avian sarcoma virus 17oncogene 237 238 975 . . . 1970 homolog M141 KIAA0215: KIAA0215 protein239 240 299 . . . 2770 M227 KIAA0878: KIAA0878 protein 241 242 336 . . .2171 M228 KIAA0882: KIAA0882 protein 243 244  <1 . . . 2776 M143KIAA1051: KIAA1051 protein 245 246  <1 . . . 1030 M405 KIAA1077:KIAA1077 protein 247 248 267 . . . 2882 M557 KIAA1181: KIAA1181 protein249 250  <1 . . . 1012 M144 KIAA1277: KIAA1277 protein 251 252  <5 . . .3079 M145 KIAA1361: KIAA1361 protein 253 254 <141 . . . 3158  M146KIAA1598: KIAA1598 protein 255 256 111 . . . 488  M147 KRT8: Keratin-8257 258  60 . . . 1511 M148 LBP: lipopolysaccharide-binding protein 259260  18 . . . 1463 M229 LDHB: lactate dehydrogenase B 261 262  85 . . .1089 M149 LIV-1: LIV-1 protein, estrogen regulated 263 264 138 . . .2387 M558 LOC118430: small breast epithelial mucin 265 266 69 . . . 341M406 LOC51242: hypothetical protein LOC51242 267 268  1 . . . 435 M230LOC57402: S100-type calcium binding protein A14 269 270 99 . . . 413M559 LPHB: lipophilin B (uteroglobin family member), 271 272 64 . . .336 prostatein-like M152 MDS024: MDS024 protein 273 274 65 . . . 838M153 ME1: malic enzyme 1, NADP(+)-dependent, 275 276 108 . . . 1826cytosolic M560 MGB1: mammaglobin 1 277 278 61 . . . 342 M458 MGB2:mammaglobin 2 279 280 65 . . . 352 M154 MGC10765: hypothetical proteinMGC10765 281 282 14 . . . 679 M155 MGC2771: hypothetical protein MGC2771283 284 185 . . . 1987 M231 MGC3038: hypothetical protein MGC3038similar to 285 286 87 . . . 548 actin related protein 2/3 complex,subunit 5 M232 MGC3077: hypothetical protein MGC3077 287 288 137 . . .703  M675 MGC9753: hypothetical protein MGC9753 289 290 1092 . . . 1814 M47 MGP: matrix Gla protein 291 292 47 . . . 358 M156 MIG: monokineinduced by gamma interferon 293 294 40 . . . 417 M157 MLN64:steroidogenic acute regulatory protein 295 296 122 . . . 1459 relatedM158 MMP11: matrix metalloproteinase 11 preproprotein; 297 298  23 . . .1489 stromelysin 3 OV52 MMP7: matrix metalloproteinase 7 (matrilysin,299 300 28 . . . 831 uterine) M407 MS4A7: membrane-spanning 4-domains,subfamily 301 302 147 . . . 869  A, member 7, variant 1 M676 MS4A7:membrane-spanning 4-domains, subfamily 303 302 118 . . . 840  A, member7, variant 2 M150 MSC: mitochondrial solute carrier, hypothetical 304305 368 . . . 652  protein PRO1278; HT015 protein M151 MST4:serine/threonine protein kinase MASK 306 307 118 . . . 1368 M159 MTHFD2:methylene tetrahydrofolate 308 309  16 . . . 1050 dehydrogenase (NAD+dependent), methenyltetrahydrofolate cyclohydrolase M669 MUC1: mucin 1,transmembrane 310 311  74 . . . 3841 M160 MYCBP: c-myc binding protein312 313 39 . . . 350 M233 MYO5A: myosin VA (heavy polypeptide 12,myoxin) 314 315 251 . . . 5818 M161 MYO6: myosin VI 316 317 140 . . .3997 M162 NAT1: N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M163 NAT1: N-acetyltransferase 1 (arylamine N- 320319 441 . . . 1313 acetyltransferase), NAT1*11B allele M677 NCALD:neurocalcin delta 321 322 121 . . . 702  M408 NDRG1: N-myc downstreamregulated protein 323 324 111 . . . 1295 M561 NDUFA8: NADH dehydrogenase(ubiquinone) 1 325 326 68 . . . 586 alpha subcomplex, 8 (19 kD, PGIV)M164 NET-6: tetraspan NET-6 protein 327 328 163 . . . 777  M165 NPY1R:neuropeptide Y receptor Y1 329 330 209 . . . 1363 M236 NY-BR-1.1: breastcancer antigen NY-BR-1.1 331 332 181 . . . 3858 M235 NY-BR-1: breastcancer antigen NY-BR-1 333 334 100 . . . 4125 OV48 OPN-a: Secretedphosphoprotein-1 (osteopontin, 335 336  1 . . . 942 bone sialoprotein)OV49 OPN-b: Secreted phosphoprotein-1 (osteopontin, 337 338 88 . . . 990bone sialoprotein) OV50 OPN-c: Secreted phosphoprotein-1 (osteopontin,339 340  1 . . . 861 bone sialoprotein) M56 OSF-2: osteoblast specificfactor 2 (fasciclin I-like) 341 342  12 . . . 2522 M176 P4HB:procollagen-proline, 2-oxoglutarate 4- 343 344  30 . . . 1556dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfideisomerase; thyroid hormone binding protein p55) M166 PAFAH1B3:platelet-activating factor 345 346 114 . . . 809  acetylhydrolase,isoform Ib, gamma subunit M409 PAR6B: PAR-6 beta 347 348  1 . . . 1119M410 PC4: activated RNA polymerase II: transcription 349 350  1 . . .384 cofactor 4 M167 PCSK1: proprotein convertase subtilisin/kexin type 1351 352 190 . . . 2451 M411 PCTA-1: prostate carcinoma tumor antigen 353354  55 . . . 1007 M412 PDCD9: programmed cell death 9 355 356  39 . . .1358 M562 PIP: prolactin-induced protein 357 358 37 . . . 477 M168 PKIB:protein kinase (cAMP-dependent, catalytic) 359 360 112 . . . 348 inhibitor beta M414 PLAUR: plasminogen activator, urokinase receptor 361362 427 . . . 1434 M169 PLU-1: putative DNA/chromatin binding motif 363364  90 . . . 4724 M170 PPARBP, PPAR binding protein, thyroid hormone365 366 236 . . . 4936 receptor interactor 2; PPARG binding protein M171PPIF: peptidylprolyl isomerase F (cyclophilin F), 367 368 72 . . . 695variant 1 M172 PPIF: peptidylprolyl isomerase F (cyclophilin F), 369 36884 . . . 707 variant 2 M173 PPIF: peptidylprolyl isomerase F(cyclophilin F), 370 371 84 . . . 659 variant 3 M174 PRLR: prolactinreceptor 372 373 285 . . . 2153 M175 PRO2000: PRO2000 protein 374 375651 . . . 1739 M177 PROML1: prominin (mouse)-like 1; hematopoietic 376377  38 . . . 2635 stem cell antigen M237 PSMB3: proteasome (prosome,macropain) subunit, 378 379 18 . . . 635 beta type, 3 M678 PSMB9:proteasome (prosome, macropain) subunit, 380 381 41 . . . 700 beta type,9 (large multifunctional protease 2) M178 PSMD3: proteasome (prosome,macropain) 26S 382 383 158 . . . 1762 subunit, non-ATPase, 3 M415PTP4A2: protein tyrosine phosphatase type IVA, 384 385 424 . . . 927 member 2 M416 RAB22B: small GTP-binding protein RAB22B 386 387 129 . . .716  M417 RAB27B: RAB27B, member RAS oncogene family 388 389 93 . . .749 M179 RAB5EP: rabaptin-5 390 391 189 . . . 2777 M180 RAMP3: receptor(calcitonin) activity modifying 392 393 30 . . . 476 protein 3precursor; calcitonin receptor-like receptor activity modifying protein3 M679 RARRES1: retinoic acid receptor responder 394 395 37 . . . 723(tazarotene induced) 1, variant 1 M680 RARRES1: retinoic acid receptorresponder 396 397 128 . . . 1012 (tazarotene induced) 1, variant 2 M91RASGRP1: RAS guanyl releasing protein 1 (calcium 398 399  <1 . . . 2351and DAG-regulated) M238 RNB6: RNB6 protein, variant 1 400 401  62 . . .1318 M418 RNB6: RNB6 protein, variant 2 402 403 125 . . . 1285 M181RPL19: ribosomal protein L19 404 405 29 . . . 619 M182 RQCD1: rcd1(required for cell differentiation, 406 407  1 . . . 900 S. pombe)homolog 1 M183 S100A8: S100 calcium-binding protein A8 408 409 56 . . .340 M239 SCD: stearoyl-CoA desaturase (delta-9-desaturase) 410 411 236 .. . 1315 M419 SCYB10: small inducible cytokine subfamily B (Cys- 412 41367 . . . 363 X-Cys), member 10 M563 SEMA3E: sema domain, immunoglobulindomain 414 415 467 . . . 2794 (Ig), short basic domain, secreted,(semaphorin) 3E M421 SERHL: kraken-like, variant 1 416 417 118 . . .1062 M422 SERHL: kraken-like, variant 2 418 419 82 . . . 693 M240SERPINA3: serine (or cysteine) proteinase inhibitor, 420 421  26 . . .1327 clade A (alpha-1 antiproteinase, antitrypsin), member 3 M564 SHARP:SMART/HDAC1 associated repressor 422 423  205 . . . 11199 protein M241SIAH2: seven in absentia (Drosophila) homolog 2, 424 425 527 . . . 1501variant 1 M619 SIAH2: seven in absentia (Drosophila) homolog 2, 426 425527 . . . 1501 variant 2 M184 SLC9A3R1: solute carrier family 9(sodium/hydrogen 427 428 213 . . . 1289 exchanger), isoform 3 regulatoryfactor 1 M185 SLPI: secretory leukocyte protease inhibitor 429 430 19 .. . 417 (antileukoproteinase), variant 1 M681 SLPI: secretory leukocyteprotease inhibitor 431 430 23 . . . 421 (antileukoproteinase), variant 2M186 SPN: asporin (LRR class 1) 432 433 247 . . . 810  M423 SQLE:squalene epoxidase 434 435 876 . . . 2600 M424 STAT4: signal transducerand activator of 436 437  82 . . . 1353 transcription 4, variant 1 M425STAT4: signal transducer and activator of 438 439  82 . . . 2328transcription 4, variant 2 M187 STC1: stanniocalcin 1 440 441 285 . . .1028 M426 STC2: stanniocalcin 2 442 443 135 . . . 1043 M188 STHM:sialyltransferase 444 445  40 . . . 1164 M565 SYTL2: synaptotagmin-like2 446 447 261 . . . 1766 M566 SYTL2: synaptotagmin-like 2, isoform a 448449 572 . . . 3304 M567 SYTL2: synaptotagmin-like 2, isoform b 450 451690 . . . 1820 M189 TAF1C: TATA box binding protein (TBP)-associated 452453 185 . . . 2794 factor, RNA polymerase I, C, 110 kD M190 TDP52: tumorprotein D52 454 455 92 . . . 646 M568 TFAP2A: transcription factor AP-2alpha (activating 456 457 282 . . . 1601 enhancer-binding protein 2alpha), variant 1 M569 TFAP2A: transcription factor AP-2 alpha(activating 458 457 282 . . . 1601 enhancer-binding protein 2 alpha),variant 2 M620 TFAP2B: transcription factor AP-2 beta (activating 459460 257 . . . 1639 enhancer binding protein 2 beta), variant 1 M621TFAP2B: transcription factor AP-2 beta (activating 461 462 257 . . .1666 enhancer binding protein 2 beta), variant 2 M242 TFF1: trefoilfactor 1 (breast cancer, estrogen- 463 464 41 . . . 295 induciblesequence expressed in) M243 TFF3: trefoil factor 3 (intestinal), variant1 465 466  2 . . . 226 M682 TFF3: trefoil factor 3 (intestinal), variant2 467 468 128 . . . 520  M191 TLN1: talin 1 469 470 127 . . . 7752 M192TRPS1: trichorhinophalangeal syndrome I 471 472 639 . . . 4484 M427UGDH: UDP-glucose dehydrogenase 473 474  79 . . . 1563 M193 unnamed gene(1) 475 476  75 . . . 1697 M194 unnamed gene (2) 477 478  23 . . . 1066M234 unnamed gene (3) 479 480 55 . . . 676 M393 unnamed gene (4) 481 482287 . . . 406  M420 unnamed gene (5) 483 484 203 . . . 1951 M428 unnamedgene (6), variant 1 485 486  75 . . . 2471 M429 unnamed gene (6),variant 2 487 488  75 . . . 1535 M622 unnamed gene (7) 489 490 579à803M93 unnamed gene (CASB619), variant 1 491 492 310 . . . 3351 M94 unnamedgene (CASB619), variant 2 493 494 310 . . . 3324 M138 unnamed gene(HSECP) 495 496 27 . . . 863 M195 VAV3: vav 3 oncogene 497 498  48 . . .2591 OV25 WFDC2: Epididymis-specific, whey-acidic protein 499 500 28 . .. 405 type, four-disulfide core M197 XBP1: X-box binding protein 1,variant 1 501 502 49 . . . 834 M244 XBP1: X-box binding protein 1,variant 2 503 504 49 . . . 834 M198 ZNF217: zinc finger protein 217 505506 272 . . . 3418

TABLE 2 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M552 AEBP1:AE-binding protein 1 1 2 140 . . . 3616 M391 ARHGEF12: Rho guanineexchange factor (GEF) 14 15  8 . . . 4642 12 M672 ASS: argininosuccinatesynthetase, transcript 16 17  76 . . . 1314 variant 1 M673 ASS:argininosuccinate synthetase, transcript 18 19  81 . . . 1319 variant 2M200 ATP5A1: ATP synthase, H+ transporting, 20 21  59 . . . 1720mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle M366AZGP1: alpha-2-glycoprotein 1, zinc 22 23  1 . . . 897 M392 BAK1:BCL2-antagonist/killer 1 24 25 201 . . . 836  M201 BGN: biglycan 28 29121 . . . 1227 M394 C1orf21: chromosome 1 open reading frame 21 32 33400 . . . 765  M202 CALM1: calmodulin 1 (phosphorylase kinase, 34 35 200. . . 649  delta) M367 CD24: CD24 antigen (small cell lung carcinoma 3839 57 . . . 299 cluster 4 antigen) M203 CDH2: cadherin 2, type 1,N-cadherin (neuronal) 42 43 102 . . . 2822 M254 CGI-96: CGI-96 protein52 53 175 . . . 1146 M553 CLECSF1: C-type (calcium dependent, 56 57 53 .. . 673 carbohydrate-recognition domain) lectin, superfamily member 1(cartilage-derived), variant 2 M204 COL10A1: collagen, type X, alpha 1(Schmid 58 59  1 . . . 2043 metaphyseal chondrodysplasia) M205 COL12A1:collagen, type XII, alpha 1, variant 1 60 61  1 . . . 9192 M618 COL12A1:collagen, type XII, alpha 1, variant 2 62 63 114 . . . 9305 M494 COL1A1:collagen, type I, alpha 1, variant 2 66 65 120 . . . 4514 M206 COL3A1:collagen, type III, alpha 1 (Ehlers-Danlos 67 68 103 . . . 4503 syndrometype IV, autosomal dominant) M101 COL5A2: collagen, type V, alpha 2 6970 139 . . . 4629 M207 COX6C: cytochrome c oxidase subunit VIc 73 74 68. . . 295 M16 CRIP1: cysteine-rich protein 1 (intestinal) 83 84  1 . . .234 M395 CSK: c-src tyrosine kinase 87 88 413 . . . 1765 M208 CTBP2:C-terminal binding protein 2, isoform 1 91 92 346 . . . 1683 M209 CTBP2:C-terminal binding protein 2, isoform 2 93 94 137 . . . 3094 M396CYP1B1: cytochrome P450, subfamily I (dioxin- 95 96 373 . . . 2004inducible), polypeptide 1 M554 DKFZP566I133: hypothetical protein 113114 134 . . . 1354 DKFZp566I133, variant 2 M555 DUSP4: dual specificityphosphatase 4 119 120 502 . . . 1686 M210 EDIL3: EGF-like repeats anddiscoidin I-like 121 122 111 . . . 1553 domains 3 M211 ENO1: enolase 1,(alpha) 123 124  95 . . . 1399 M114 ESR1: estrogen receptor 1 127 128361 . . . 2148 M397 FGF7: fibroblast growth factor 7 (keratinocyte 137138 446 . . . 1030 growth factor) M212 FKSG12: pancreas tumor-relatedprotein 141 142 238 . . . 1125 M398 FLJ20171: hypothetical proteinFLJ20171 151 152  58 . . . 1134 M514 FLJ20940: hypothetical proteinFLJ20940 153 154 236 . . . 742  M399 FLJ21174: hypothetical proteinFLJ21174 155 156 234 . . . 881  M400 FLJ22418: hypothetical proteinFLJ22418 163 164 71 . . . 919 M213 FXYD3: FXYD domain-containing iontransport 165 166 176 . . . 439  regulator 3, isoform 1 M214 FXYD3: FXYDdomain-containing ion transport 167 168 260 . . . 601  regulator 3,isoform 2 M215 GABRP: gamma-aminobutyric acid (GABA) A 171 172 157 . . .1479 receptor, pi M216 GATA3: GATA-binding protein 3, variant 1 175 176461 . . . 1792 M217 GATA3: GATA-binding protein 3, variant 2 177 176 461. . . 1792 M218 GATA3: GATA-binding protein 3, variant 3 178 176 152 . .. 1483 M271 GOLPH2: golgi phosphoprotein 2 183 184 151 . . . 1353 M219GPD2: glycerol-3-phosphate dehydrogenase 2 185 186 124 . . . 2307(mitochondrial) M495 GSTP1: glutathione S-transferase pi 191 192 30 . .. 662 M220 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 193 194 520 .. . 2592 variant 1 M221 GUCY1A3: guanylate cyclase 1, soluble, alpha 3,195 194 386 . . . 2458 variant 2 M222 GUCY1A3: guanylate cyclase 1,soluble, alpha 3, 196 194 407 . . . 2479 variant 3 M199 HAG-2: anteriorgradient 2 (Xenopus laevis) 199 200 59 . . . 586 homolog M225 HAG-3:anterior gradient protein 3, variant 2 203 204 116 . . . 129  M273HMGCS2: 3-hydroxy-3-methylglutaryl-Coenzyme A 207 208  52 . . . 1578synthase 2 (mitochondrial) M674 HN1: hematological and neurologicalexpressed 1 209 210 104 . . . 568  M223 HNF3A: hepatocyte nuclear factor3, alpha 211 212  88 . . . 1509 M401 HSCP1: serine carboxypeptidase 1precursor 219 220  33 . . . 1391 protein M224 HSPC155: hypotheticalprotein HSPC155 221 222 241 . . . 744  M402 HSPD1: heat shock 60 kDprotein 1 (chaperonin) 223 224  25 . . . 1746 M403 IGF1R: insulin-likegrowth factor 1 receptor 225 226  46 . . . 4149 M404 IL6ST: interleukin6 signal transducer (gp130, 229 230 256 . . . 3012 oncostatin Mreceptor) M34 INHBA: Inhibin, beta-1 (activin A, activin AB alpha 231232  86 . . . 1366 polypeptide) M226 JCL-1: hepatocellular carcinomaassociated 235 236  70 . . . 1890 protein; breast cancer associated gene1 M556 JUN: v-jun avian sarcoma virus 17 oncogene 237 238 975 . . . 1970homolog M227 KIAA0878: KIAA0878 protein 241 242 336 . . . 2171 M228KIAA0882: KIAA0882 protein 243 244  <1 . . . 2776 M557 KIAA1181:KIAA1181 protein 249 250  <1 . . . 1012 M229 LDHB: lactate dehydrogenaseB 261 262  85 . . . 1089 M149 LIV-1: LIV-1 protein, estrogen regulated263 264 138 . . . 2387 M558 LOC118430: small breast epithelial mucin 265266 69 . . . 341 M406 LOC51242: hypothetical protein LOC51242 267 268  1. . . 435 M230 LOC57402: S100-type calcium binding protein A14 269 27099 . . . 413 M559 LPHB: lipophilin B (uteroglobin family member), 271272 64 . . . 336 prostatein-like M560 MGB1: mammaglobin 1 277 278 61 . .. 342 M458 MGB2: mammaglobin 2 279 280 65 . . . 352 M155 MGC2771:hypothetical protein MGC2771 283 284 185 . . . 1987 M231 MGC3038:hypothetical protein MGC3038 similar 285 286 87 . . . 548 to actinrelated protein 2/3 complex, subunit 5 M232 MGC3077: hypotheticalprotein MGC3077 287 288 137 . . . 703  M675 MGC9753: hypotheticalprotein MGC9753 289 290 1092 . . . 1814  M47 MGP: matrix Gla protein 291292 47 . . . 358 M407 MS4A7: membrane-spanning 4-domains, subfamily 301302 147 . . . 869  A, member 7, variant 1 M676 MS4A7: membrane-spanning4-domains, subfamily 303 302 118 . . . 840  A, member 7, variant 2 M669MUC1: mucin 1, transmembrane 310 311  74 . . . 3841 M233 MYO5A: myosinVA (heavy polypeptide 12, 314 315 251 . . . 5818 myoxin) M162 NAT1:N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M677 NCALD: neurocalcin delta 321 322 121 . . . 702 M408 NDRG1: N-myc downstream regulated protein 323 324 111 . . . 1295M561 NDUFA8: NADH dehydrogenase (ubiquinone) 1 325 326 68 . . . 586alpha subcomplex, 8 (19 kD, PGIV) M164 NET-6: tetraspan NET-6 protein327 328 163 . . . 777  M236 NY-BR-1.1: breast cancer antigen NY-BR-1.1331 332 181 . . . 3858 M235 NY-BR-1: breast cancer antigen NY-BR-1 333334 100 . . . 4125 M56 OSF-2: osteoblast specific factor 2 (fasciclinI-like) 341 342  12 . . . 2522 M409 PAR6B: PAR-6 beta 347 348  1 . . .1119 M410 PC4: activated RNA polymerase II: transcription 349 350  1 . .. 384 cofactor 4 M412 PDCD9: programmed cell death 9 355 356  39 . . .1358 M562 PIP: prolactin-induced protein 357 358 37 . . . 477 M414PLAUR: plasminogen activator, urokinase receptor 361 362 427 . . . 1434M237 PSMB3: proteasome (prosome, macropain) 378 379 18 . . . 635subunit, beta type, 3 M678 PSMB9: proteasome (prosome, macropain) 380381 41 . . . 700 subunit, beta type, 9 (large multifunctional protease2) M415 PTP4A2: protein tyrosine phosphatase type IVA, 384 385 424 . . .927  member 2 M416 RAB22B: small GTP-binding protein RAB22B 386 387 129. . . 716  M417 RAB27B: RAB27B, member RAS oncogene family 388 389 93 .. . 749 M679 RARRES1: retinoic acid receptor responder 394 395 37 . . .723 (tazarotene induced) 1, variant 1 M680 RARRES1: retinoic acidreceptor responder 396 397 128 . . . 1012 (tazarotene induced) 1,variant 2 M238 RNB6: RNB6 protein, variant 1 400 401  62 . . . 1318 M418RNB6: RNB6 protein, variant 2 402 403 125 . . . 1285 M239 SCD:stearoyl-CoA desaturase (delta-9- 410 411 236 . . . 1315 desaturase)M419 SCYB10: small inducible cytokine subfamily B 412 413 67 . . . 363(Cys-X-Cys), member 10 M563 SEMA3E: sema domain, immunoglobulin domain414 415 467 . . . 2794 (Ig), short basic domain, secreted, (semaphorin)3E M421 SERHL: kraken-like, variant 1 416 417 118 . . . 1062 M422 SERHL:kraken-like, variant 2 418 419 82 . . . 693 M240 SERPINA3: serine (orcysteine) proteinase 420 421  26 . . . 1327 inhibitor, clade A (alpha-1antiproteinase, antitrypsin), member 3 M564 SHARP: SMART/HDAC1associated repressor 422 423  205 . . . 11199 protein M241 SIAH2: sevenin absentia (Drosophila) homolog 2, 424 425 527 . . . 1501 variant 1M619 SIAH2: seven in absentia (Drosophila) homolog 2, 426 425 527 . . .1501 variant 2 M681 SLPI: secretory leukocyte protease inhibitor 431 43023 . . . 421 (antileukoproteinase), variant 2 M423 SQLE: squaleneepoxidase 434 435 876 . . . 2600 M424 STAT4: signal transducer andactivator of 436 437  82 . . . 1353 transcription 4, variant 1 M425STAT4: signal transducer and activator of 438 439  82 . . . 2328transcription 4, variant 2 M426 STC2: stanniocalcin 2 442 443 135 . . .1043 M565 SYTL2: synaptotagmin-like 2 446 447 261 . . . 1766 M566 SYTL2:synaptotagmin-like 2, isoform a 448 449 572 . . . 3304 M567 SYTL2:synaptotagmin-like 2, isoform b 450 451 690 . . . 1820 M568 TFAP2A:transcription factor AP-2 alpha (activating 456 457 282 . . . 1601enhancer-binding protein 2 alpha), variant 1 M569 TFAP2A: transcriptionfactor AP-2 alpha (activating 458 457 282 . . . 1601 enhancer-bindingprotein 2 alpha), variant 2 M620 TFAP2B: transcription factor AP-2 beta(activating 459 460 257 . . . 1639 enhancer binding protein 2 beta),variant 1 M621 TFAP2B: transcription factor AP-2 beta (activating 461462 257 . . . 1666 enhancer binding protein 2 beta), variant 2 M242TFF1: trefoil factor 1 (breast cancer, estrogen- 463 464 41 . . . 295inducible sequence expressed in) M243 TFF3: trefoil factor 3(intestinal), variant 1 465 466  2 . . . 226 M192 TRPS1:trichorhinophalangeal syndrome I 471 472 639 . . . 4484 M427 UGDH:UDP-glucose dehydrogenase 473 474  79 . . . 1563 M194 unnamed gene (2)477 478  23 . . . 1066 M234 unnamed gene (3) 479 480 55 . . . 676 M393unnamed gene (4) 481 482 287 . . . 406  M420 unnamed gene (5) 483 484203 . . . 1951 M428 unnamed gene (6), variant 1 485 486  75 . . . 2471M429 unnamed gene (6), variant 2 487 488  75 . . . 1535 M622 unnamedgene (7) 489 490 579à803 OV25 WFDC2: Epididymis-specific, whey-acidicprotein 499 500 28 . . . 405 type, four-disulfide core M244 XBP1: X-boxbinding protein 1, variant 2 503 504 49 . . . 834

TABLE 3 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M83 AKR1C1:aldo-keto reductase family 1, member C1 3 4  7 . . . 978 (20-alpha(3-alpha)-hydroxysteroid dehydrogenase) M84 AKR1C3: aldo-keto reductasefamily 1, member C3 5 6  1 . . . 972 (3-alpha hydroxysteroiddehydrogenase, type II) M85 ALDOB: aldolase B, fructose-bisphosphate 7 8126 . . . 1220 M86 AQP3: Aquaporin 3, variant 1 9 10 65 . . . 943 M87AQP3: Aquaporin 3, variant 2 11 10 65 . . . 943 M88 AREG: amphiregulin(schwannoma-derived growth 12 13 210 . . . 968  factor) M89 BF:B-factor, properdin 26 27  41 . . . 2335 M90 BMI1: murine leukemia viral(bmi-1) oncogene 30 31 480 . . . 1460 homolog M92 CART: cocaine- andamphetamine-regulated 36 37 20 . . . 370 transcript M95 CDC2: celldivision cycle 2, G1 to S and G2 to M 40 41 127 . . . 1020 M96 CEGP1:CEGP1 protein 44 45  81 . . . 3080 M97 CEZANNE: zinc finger proteinCezanne 46 47 155 . . . 2731 M98 CGI-52: CGI-52 protein, similar to 4849 277 . . . 1356 phosphatidylcholine transfer protein 2 M99 CGI-72:CGI-72 protein 50 51  70 . . . 1401 M100 CLECSF1: C-type (calciumdependent, 54 55 80 . . . 673 carbohydrate-recognition domain) lectin,superfamily member 1 (cartilage-derived), variant 1 M12 COL1A1:collagen, type I, alpha 1, variant 1 64 65 120 . . . 4514 M102 COMP:cartilage oligomeric matrix protein 71 72  26 . . . 2299(pseudoachondroplasia, epiphyseal dysplasia 1, multiple) OV7 CP:ceruloplasmin (ferroxidase), variant 1 75 76  <1 . . . 2561 OV8 CP:ceruloplasmin (ferroxidase), variant 2 77 78  1 . . . 3198 OV66 CP:ceruloplasmin (ferroxidase), variant 3 79 80  1 . . . 3210 M103 CRABP2:cellular retinoic acid-binding protein 2 81 82 138 . . . 554  M104CrkRS: CDC2-related protein kinase 7 85 86  34 . . . 4506 M105 CSPG2:chondroitin sulfate proteoglycan 2 89 90 267 . . . 7496 (versican) M106CYP24: cytochrome P450, subfamily XXIV (vitamin 97 98 405 . . . 1946 D24-hydroxylase) OV40 DD96: Epithelial protein up-regulated in carcinoma,99 100 202 . . . 546  membrane associated protein 17 M142 DEME-6: DEME-6protein 101 102  <1 . . . 1725 M107 DJ167A19: hypothetical proteinDJ167A19.1 103 104  1 . . . 921 M108 DKFZP564D166: putativeankyrin-repeat 105 106  95 . . . 3400 containing protein M109DKFZP564D206: hypothetical protein 107 108  <1 . . . 405 DKFZP564D206M82 DKFZp564I1922: adlican 109 110  1 . . . 8487 M110 DKFZP566I133:hypothetical protein 111 112 134 . . . 1354 DKFZp566I133, variant 1 M111DNAJL1: hypothetical protein similar to mouse 115 116 203 . . . 1225DnajI1 M112 DRIL1: dead ringer (Drosophila)-like 1 117 118 201 . . .1982 M113 ERBB2: v-erb-b2 avian erythroblastic leukemia 125 126 151 . .. 3919 viral oncogene homolog 2 (neuro/glioblastoma derived oncogenehomolog) M116 FABP7: B-FABP, fatty acid binding protein 7 131 132 77 . .. 475 M118 FAP: fibroblast activation protein, alpha 135 136 209 . . .2491 M119 FKBP4: FK506-binding protein 4 139 140 100 . . . 1479 M120FLJ12425: hypothetical protein FLJ12425 143 144 42 . . . 335 M121FLJ12910: hypothetical protein FLJ12910 145 146 260 . . . 1585 M122FLJ13187: hypothetical protein FLJ13187 147 148 98 . . . 847 M123FLJ14103: hypothetical protein FLJ14103 149 150 76 . . . 624 M124FLJ21213: hypothetical protein FLJ21213 157 158  3 . . . 809 M125FLJ21879: hypothetical protein FLJ21879 159 160  75 . . . 1043 M126FLJ22002: hypothetical protein FLJ22002 161 162 116 . . . 784  M127G1P3: interferon, alpha-inducible protein (clone IFI- 169 170 108 . . .500  6-16) M128 GATA2: GATA-binding protein 2 173 174 194 . . . 1618M129 GNLY: granulysin, isoform 519 179 180 281 . . . 670  M130 GNLY:granulysin, isoform NKG5 181 182 129 . . . 566  M132 GRIA2: glutamatereceptor, ionotropic, AMPA 2 189 190 161 . . . 2812 M133 GZMA: GranzymeA (Cytotoxic T-lymphocyte- 197 198 39 . . . 827 associated serineesterase-3; Hanukah factor serine protease); CTL tryptase M134 HDAC2:histone deacetylase 2 205 206 205 . . . 1671 M135 HOXB2: homeo box B2213 214  79 . . . 1149 M136 HPD: 4-hydroxyphenylpyruvate dioxygenase 215216  26 . . . 1207 M137 HPGD: hydroxyprostaglandin dehydrogenase 15- 217218 18 . . . 818 (NAD) M139 IGSF1: IGCD1, IGDC1, KIAA036, immunoglobulin227 228  81 . . . 4091 superfamily, member 1 M140 ISG15:interferon-stimulated protein, 15 kDa 233 234 76 . . . 573 M141KIAA0215: KIAA0215 protein 239 240 299 . . . 2770 M143 KIAA1051:KIAA1051 protein 245 246  <1 . . . 1030 M144 KIAA1277: KIAA1277 protein251 252  <5 . . . 3079 M145 KIAA1361: KIAA1361 protein 253 254 <141 . .. 3158  M146 KIAA1598: KIAA1598 protein 255 256 111 . . . 488  M147KRT8: Keratin-8 257 258  60 . . . 1511 M148 LBP:lipopolysaccharide-binding protein 259 260  18 . . . 1463 M152 MDS024:MDS024 protein 273 274 65 . . . 838 M153 ME1: malic enzyme 1,NADP(+)-dependent, 275 276 108 . . . 1826 cytosolic M154 MGC10765:hypothetical protein MGC10765 281 282 14 . . . 679 M156 MIG: monokineinduced by gamma interferon 293 294 40 . . . 417 M157 MLN64:steroidogenic acute regulatory protein 295 296 122 . . . 1459 relatedOV52 MMP7: matrix metalloproteinase 7 (matrilysin, 299 300 28 . . . 831uterine) M150 MSC: mitochondrial solute carrier, hypothetical 304 305368 . . . 652  protein PRO1278; HT015 protein M151 MST4:serine/threonine protein kinase MASK 306 307 118 . . . 1368 M160 MYCBP:c-myc binding protein 312 313 39 . . . 350 M161 MYO6: myosin VI 316 317140 . . . 3997 M165 NPY1R: neuropeptide Y receptor Y1 329 330 209 . . .1363 OV48 OPN-a: Secreted phosphoprotein-1 (osteopontin, 335 336  1 . .. 942 bone sialoprotein) OV49 OPN-b: Secreted phosphoprotein-1(osteopontin, 337 338 88 . . . 990 bone sialoprotein) OV50 OPN-c:Secreted phosphoprotein-1 (osteopontin, 339 340  1 . . . 861 bonesialoprotein) M176 P4HB: procollagen-proline, 2-oxoglutarate 4- 343 344 30 . . . 1556 dioxygenase (proline 4-hydroxylase), beta polypeptide(protein disulfide isomerase; thyroid hormone binding protein p55) M166PAFAH1B3: platelet-activating factor 345 346 114 . . . 809 acetylhydrolase, isoform Ib, gamma subunit M167 PCSK1: proproteinconvertase subtilisin/kexin type 1 351 352 190 . . . 2451 M168 PKIB:protein kinase (cAMP-dependent, catalytic) 359 360 112 . . . 348 inhibitor beta M169 PLU-1: putative DNA/chromatin binding motif 363 364 90 . . . 4724 M170 PPARBP, PPAR binding protein, thyroid hormone 365366 236 . . . 4936 receptor interactor 2; PPARG binding protein M171PPIF: peptidylprolyl isomerase F (cyclophilin F), 367 368 72 . . . 695variant 1 M172 PPIF: peptidylprolyl isomerase F (cyclophilin F), 369 36884 . . . 707 variant 2 M173 PPIF: peptidylprolyl isomerase F(cyclophilin F), 370 371 84 . . . 659 variant 3 M174 PRLR: prolactinreceptor 372 373 285 . . . 2153 M175 PRO2000: PRO2000 protein 374 375651 . . . 1739 M177 PROML1: prominin (mouse)-like 1; hematopoietic 376377  38 . . . 2635 stem cell antigen M179 RAB5EP: rabaptin-5 390 391 189. . . 2777 M180 RAMP3: receptor (calcitonin) activity modifying 392 39330 . . . 476 protein 3 precursor; calcitonin receptor-like receptoractivity modifying protein 3 M91 RASGRP1: RAS guanyl releasing protein 1398 399  <1 . . . 2351 (calcium and DAG-regulated) M182 RQCD1: rcd1(required for cell differentiation, 406 407  1 . . . 900 S. pombe)homolog 1 M183 S100A8: S100 calcium-binding protein A8 408 409 56 . . .340 M184 SLC9A3R1: solute carrier family 9 427 428 213 . . . 1289(sodium/hydrogen exchanger), isoform 3 regulatory factor 1 M185 SLPI:secretory leukocyte protease inhibitor 429 430 19 . . . 417(antileukoproteinase), variant 1 M186 SPN: asporin (LRR class 1) 432 433247 . . . 810  M188 STHM: sialyltransferase 444 445  40 . . . 1164 M189TAF1C: TATA box binding protein (TBP)- 452 453 185 . . . 2794 associatedfactor, RNA polymerase I, C, 110 kD M190 TDP52: tumor protein D52 454455 92 . . . 646 M682 TFF3: trefoil factor 3 (intestinal), variant 2 467468 128 . . . 520  M191 TLN1: talin 1 469 470 127 . . . 7752 M193unnamed gene (1) 475 476  75 . . . 1697 M93 unnamed gene (CASB619),variant 1 491 492 310 . . . 3351 M94 unnamed gene (CASB619), variant 2493 494 310 . . . 3324 M138 unnamed gene (HSECP) 495 496 27 . . . 863M195 VAV3: vav 3 oncogene 497 498  48 . . . 2591 M197 XBP1: X-boxbinding protein 1, variant 1 501 502 49 . . . 834 M198 ZNF217: zincfinger protein 217 505 506 272 . . . 3418

TABLE 4 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M115 F2R:coagulation factor II (thrombin) receptor 129 130 345 . . . 1622 M117FACL2: fatty-acid-Coenzyme A ligase, long-chain 2 133 134  14 . . . 2110M131 GPI: glucose phosphate isomerase 187 188  16 . . . 1692 M196 HAG-3:anterior gradient protein 3, variant 1 201 202 49 . . . 549 M158 MMP11:matrix metalloproteinase 11 preproprotein; 297 298  23 . . . 1489stromelysin 3 M159 MTHFD2: methylene tetrahydrofolate 308 309  16 . . .1050 dehydrogenase (NAD+ dependent), methenyltetrahydrofolatecyclohydrolase M163 NAT1: N-acetyltransferase 1 (arylamine N- 320 319441 . . . 1313 acetyltransferase), NAT1*11B allele M178 PSMD3:proteasome (prosome, macropain) 26S 382 383 158 . . . 1762 subunit,non-ATPase, 3 M181 RPL19: ribosomal protein L19 404 405 29 . . . 619M187 STC1: stanniocalcin 1 440 441 285 . . . 1028

TABLE 5 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M552 AEBP1:AE-binding protein 1 1 2 140 . . . 3616 M85 ALDOB: aldolase B,fructose-bisphosphate 7 8 126 . . . 1220 M88 AREG: amphiregulin(schwannoma-derived growth 12 13 210 . . . 968  factor) M366 AZGP1:alpha-2-glycoprotein 1, zinc 22 23  1 . . . 897 M89 BF: B-factor,properdin 26 27  41 . . . 2335 M201 BGN: biglycan 28 29 121 . . . 1227M90 BMI1: murine leukemia viral (bmi-1) oncogene 30 31 480 . . . 1460homolog M92 CART: cocaine- and amphetamine-regulated 36 37 20 . . . 370transcript M203 CDH2: cadherin 2, type 1, N-cadherin (neuronal) 42 43102 . . . 2822 M96 CEGP1: CEGP1 protein 44 45  81 . . . 3080 M97CEZANNE: zinc finger protein Cezanne 46 47 155 . . . 2731 M98 CGI-52:CGI-52 protein, similar to 48 49 277 . . . 1356 phosphatidylcholinetransfer protein 2 M99 CGI-72: CGI-72 protein 50 51  70 . . . 1401 M100CLECSF1: C-type (calcium dependent, 54 55 80 . . . 673carbohydrate-recognition domain) lectin, superfamily member 1(cartilage-derived), variant 1 M553 CLECSF1: C-type (calcium dependent,56 57 53 . . . 673 carbohydrate-recognition domain) lectin, superfamilymember 1 (cartilage-derived), variant 2 M204 COL10A1: collagen, type X,alpha 1 (Schmid 58 59  1 . . . 2043 metaphyseal chondrodysplasia) M205COL12A1: collagen, type XII, alpha 1, variant 1 60 61  1 . . . 9192 M618COL12A1: collagen, type XII, alpha 1, variant 2 62 63 114 . . . 9305 M12COL1A1: collagen, type I, alpha 1, variant 1 64 65 120 . . . 4514 M494COL1A1: collagen, type I, alpha 1, variant 2 66 65 120 . . . 4514 M206COL3A1: collagen, type III, alpha 1 (Ehlers-Danlos 67 68 103 . . . 4503syndrome type IV, autosomal dominant) M101 COL5A2: collagen, type V,alpha 2 69 70 139 . . . 4629 M102 COMP: cartilage oligomeric matrixprotein 71 72  26 . . . 2299 (pseudoachondroplasia, epiphyseal dysplasia1, multiple) M207 COX6C: cytochrome c oxidase subunit VIc 73 74 68 . . .295 OV7 CP: ceruloplasmin (ferroxidase), variant 1 75 76  <1 . . . 2561OV8 CP: ceruloplasmin (ferroxidase), variant 2 77 78  1 . . . 3198 OV66CP: ceruloplasmin (ferroxidase), variant 3 79 80  1 . . . 3210 M103CRABP2: cellular retinoic acid-binding protein 2 81 82 138 . . . 554 M16 CRIP1: cysteine-rich protein 1 (intestinal) 83 84  1 . . . 234 M105CSPG2: chondroitin sulfate proteoglycan 2 89 90 267 . . . 7496(versican) M208 CTBP2: C-terminal binding protein 2, isoform 1 91 92 346. . . 1683 M209 CTBP2: C-terminal binding protein 2, isoform 2 93 94 137. . . 3094 OV40 DD96: Epithelial protein up-regulated in carcinoma, 99100 202 . . . 546  membrane associated protein 17 M142 DEME-6: DEME-6protein 101 102  <1 . . . 1725 M107 DJ167A19: hypothetical proteinDJ167A19.1 103 104  1 . . . 921 M108 DKFZP564D166: putativeankyrin-repeat containing 105 106  95 . . . 3400 protein M82DKFZp564I1922: adlican 109 110 ·1 . . . 8487 M110 DKFZP566I133:hypothetical protein 111 112 134 . . . 1354 DKFZp566I133, variant 1 M554DKFZP566I133: hypothetical protein 113 114 134 . . . 1354 DKFZp566I133,variant 2 M111 DNAJL1: hypothetical protein similar to mouse 115 116 203. . . 1225 DnajI1 M555 DUSP4: dual specificity phosphatase 4 119 120 502. . . 1686 M210 EDIL3: EGF-like repeats and discoidin I-like 121 122 111. . . 1553 domains 3 M114 ESR1: estrogen receptor 1 127 128 361 . . .2148 M118 FAP: fibroblast activation protein, alpha 135 136 209 . . .2491 M119 FKBP4: FK506-binding protein 4 139 140 100 . . . 1479 M212FKSG12: pancreas tumor-related protein 141 142 238 . . . 1125 M120FLJ12425: hypothetical protein FLJ12425 143 144 42 . . . 335 M121FLJ12910: hypothetical protein FLJ12910 145 146 260 . . . 1585 M122FLJ13187: hypothetical protein FLJ13187 147 148 98 . . . 847 M123FLJ14103: hypothetical protein FLJ14103 149 150 76 . . . 624 M398FLJ20171: hypothetical protein FLJ20171 151 152  58 . . . 1134 M124FLJ21213: hypothetical protein FLJ21213 157 158  3 . . . 809 M125FLJ21879: hypothetical protein FLJ21879 159 160  75 . . . 1043 M126FLJ22002: hypothetical protein FLJ22002 161 162 116 . . . 784  M213FXYD3: FXYD domain-containing ion transport 165 166 176 . . . 439 regulator 3, isoform 1 M214 FXYD3: FXYD domain-containing ion transport167 168 260 . . . 601  regulator 3, isoform 2 M127 G1P3: interferon,alpha-inducible protein (clone IFI- 169 170 108 . . . 500  6-16) M216GATA3: GATA-binding protein 3, variant 1 175 176 461 . . . 1792 M217GATA3: GATA-binding protein 3, variant 2 177 176 461 . . . 1792 M218GATA3: GATA-binding protein 3, variant 3 178 176 152 . . . 1483 M271GOLPH2: golgi phosphoprotein 2 183 184 151 . . . 1353 M219 GPD2:glycerol-3-phosphate dehydrogenase 2 185 186 124 . . . 2307(mitochondrial) M132 GRIA2: glutamate receptor, ionotropic, AMPA 2 189190 161 . . . 2812 M199 HAG-2: anterior gradient 2 (Xenopus laevis) 199200 59 . . . 586 homolog M196 HAG-3: anterior gradient protein 3,variant 1 201 202 49 . . . 549 M225 HAG-3: anterior gradient protein 3,variant 2 203 204 116 . . . 129  M223 HNF3A: hepatocyte nuclear factor3, alpha 211 212  88 . . . 1509 M135 HOXB2: homeo box B2 213 214  79 . .. 1149 M224 HSPC155: hypothetical protein HSPC155 221 222 241 . . . 744 M403 IGF1R: insulin-like growth factor 1 receptor 225 226  46 . . . 4149M34 INHBA: Inhibin, beta-1 (activin A, activin AB alpha 231 232  86 . .. 1366 polypeptide) M140 ISG15: interferon-stimulated protein, 15 kDa233 234 76 . . . 573 M226 JCL-1: hepatocellular carcinoma associatedprotein; 235 236  70 . . . 1890 breast cancer associated gene 1 M556JUN: v-jun avian sarcoma virus 17 oncogene 237 238 975 . . . 1970homolog M141 KIAA0215: KIAA0215 protein 239 240 299 . . . 2770 M227KIAA0878: KIAA0878 protein 241 242 336 . . . 2171 M228 KIAA0882:KIAA0882 protein 243 244  <1 . . . 2776 M143 KIAA1051: KIAA1051 protein245 246  <1 . . . 1030 M405 KIAA1077: KIAA1077 protein 247 248 267 . . .2882 M557 KIAA1181: KIAA1181 protein 249 250  <1 . . . 1012 M146KIAA1598: KIAA1598 protein 255 256 111 . . . 488  M147 KRT8: Keratin-8257 258  60 . . . 1511 M149 LIV-1: LIV-1 protein, estrogen regulated 263264 138 . . . 2387 M559 LPHB: lipophilin B (uteroglobin family member),271 272 64 . . . 336 prostatein-like M560 MGB1: mammaglobin 1 277 278 61. . . 342 M458 MGB2: mammaglobin 2 279 280 65 . . . 352 M154 MGC10765:hypothetical protein MGC10765 281 282 14 . . . 679 M155 MGC2771:hypothetical protein MGC2771 283 284 185 . . . 1987 M231 MGC3038:hypothetical protein MGC3038 similar to 285 286 87 . . . 548 actinrelated protein ⅔ complex, subunit 5 M232 MGC3077: hypothetical proteinMGC3077 287 288 137 . . . 703  M47 MGP: matrix Gla protein 291 292 47 .. . 358 M156 MIG: monokine induced by gamma interferon 293 294 40 . . .417 M157 MLN64: steroidogenic acute regulatory protein 295 296 122 . . .1459 related M158 MMP11: matrix metalloproteinase 11 preproprotein; 297298  23 . . . 1489 stromelysin 3 M160 MYCBP: c-myc binding protein 312313 39 . . . 350 M161 MYO6: myosin VI 316 317 140 . . . 3997 M162 NAT1:N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M163 NAT1: N-acetyltransferase 1 (arylamine N- 320319 441 . . . 1313 acetyltransferase), NAT1*11B allele M561 NDUFA8: NADHdehydrogenase (ubiquinone) 1 325 326 68 . . . 586 alpha subcomplex, 8(19 kD, PGIV) M164 NET-6: tetraspan NET-6 protein 327 328 163 . . . 777 M165 NPY1R: neuropeptide Y receptor Y1 329 330 209 . . . 1363 M236NY-BR-1.1: breast cancer antigen NY-BR-1.1 331 332 181 . . . 3858 M235NY-BR-1: breast cancer antigen NY-BR-1 333 334 100 . . . 4125 OV48OPN-a: Secreted phosphoprotein-1 (osteopontin, 335 336  1 . . . 942 bonesialoprotein) OV49 OPN-b: Secreted phosphoprotein-1 (osteopontin, 337338 88 . . . 990 bone sialoprotein) OV50 OPN-c: Secretedphosphoprotein-1 (osteopontin, 339 340  1 . . . 861 bone sialoprotein)M56 OSF-2: osteoblast specific factor 2 (fasciclin I-like) 341 342  12 .. . 2522 M176 P4HB: procollagen-proline, 2-oxoglutarate 4- 343 344  30 .. . 1556 dioxygenase (proline 4-hydroxylase), beta polypeptide (proteindisulfide isomerase; thyroid hormone binding protein p55) M166 PAFAH1B3:platelet-activating factor 345 346 114 . . . 809  acetylhydrolase,isoform lb, gamma subunit M409 PAR6B: PAR-6 beta 347 348  1 . . . 1119M410 PC4: activated RNA polymerase II: transcription 349 350  1 . . .384 cofactor 4 M167 PCSK1: proprotein convertase subtilisin/kexin type 1351 352 190 . . . 2451 M411 PCTA-1: prostate carcinoma tumor antigen 353354  55 . . . 1007 M412 PDCD9: programmed cell death 9 355 356  39 . . .1358 M562 PIP: prolactin-induced protein 357 358  37 . . . 477 M168PKIB: protein kinase (cAMP-dependent, catalytic) 359 360 112 . . . 348 inhibitor beta M414 PLAUR: plasminogen activator, urokinase receptor 361362 427 . . . 1434 M169 PLU-1: putative DNA/chromatin binding motif 363364  90 . . . 4724 M172 PPIF: peptidylprolyl isomerase F (cyclophilinF), 369 368 84 . . . 707 variant 2 M174 PRLR: prolactin receptor 372 373285 . . . 2153 M175 PRO2000: PRO2000 protein 374 375 651 . . . 1739 M415PTP4A2: protein tyrosine phosphatase type IVA, 384 385 424 . . . 927 member 2 M416 RAB22B: small GTP-binding protein RAB22B 386 387 129 . . .716  M417 RAB27B: RAB27B, member RAS oncogene family 388 389 93 . . .749 M179 RAB5EP: rabaptin-5 390 391 189 . . . 2777 M238 RNB6: RNB6protein, variant 1 400 401  62 . . . 1318 M419 SCYB10: small induciblecytokine subfamily B (Cys- 412 413 67 . . . 363 X-Cys), member 10 M563SEMA3E: sema domain, immunoglobulin domain 414 415 467 . . . 2794 (lg),short basic domain, secreted, (semaphorin) 3E M240 SERPINA3: serine (orcysteine) proteinase inhibitor, 420 421  26 . . . 1327 clade A (alpha-1antiproteinase, antitrypsin), member 3 M564 SHARP: SMART/HDAC1associated repressor 422 423  205 . . . 11199 protein M241 SIAH2: sevenin absentia (Drosophila) homolog 2, 424 425 527 . . . 1501 variant 1M619 SIAH2: seven in absentia (Drosophila) homolog 2, 426 425 527 . . .1501 variant 2 M184 SLC9A3R1: solute carrier family 9 (sodium/hydrogen427 428 213 . . . 1289 exchanger), isoform 3 regulatory factor 1 M186SPN: asporin (LRR class 1) 432 433 247 . . . 810  M423 SQLE: squaleneepoxidase 434 435 876 . . . 2600 M426 STC2: stanniocalcin 2 442 443 135. . . 1043 M188 STHM: sialyltransferase 444 445  40 . . . 1164 M565SYTL2: synaptotagmin-like 2 446 447 261 . . . 1766 M566 SYTL2:synaptotagmin-like 2, isoform a 448 449 572 . . . 3304 M567 SYTL2:synaptotagmin-like 2, isoform b 450 451 690 . . . 1820 M190 TDP52: tumorprotein D52 454 455 92 . . . 646 M568 TFAP2A: transcription factor AP-2alpha (activating 456 457 282 . . . 1601 enhancer-binding protein 2alpha), variant 1 M569 TFAP2A: transcription factor AP-2 alpha(activating 458 457 282 . . . 1601 enhancer-binding protein 2 alpha),variant 2 M620 TFAP2B: transcription factor AP-2 beta (activating 459460 257 . . . 1639 enhancer binding protein 2 beta), variant 1 M621TFAP2B: transcription factor AP-2 beta (activating 461 462 257 . . .1666 enhancer binding protein 2 beta), variant 2 M242 TFF1: trefoilfactor 1 (breast cancer, estrogen- 463 464 41 . . . 295 induciblesequence expressed in) M243 TFF3: trefoil factor 3 (intestinal), variant1 465 466  2 . . . 226 M682 TFF3: trefoil factor 3 (intestinal), variant2 467 468 128 . . . 520  M192 TRPS1: trichorhinophalangeal syndrome I471 472 639 . . . 4484 M427 UGDH: UDP-glucose dehydrogenase 473 474  79. . . 1563 M193 unnamed gene (1) 475 476  75 . . . 1697 M194 unnamedgene (2) 477 478  23 . . . 1066 M420 unnamed gene (5) 483 484 203 . . .1951 M428 unnamed gene (6), variant 1 485 486  75 . . . 2471 M429unnamed gene (6), variant 2 487 488  75 . . . 1535 M622 unnamed gene (7)489 490 579à803 M93 unnamed gene (CASB619), variant 1 491 492 310 . . .3351 M94 unnamed gene (CASB619), variant 2 493 494 310 . . . 3324 M138unnamed gene (HSECP) 495 496 27 . . . 863 M195 VAV3: vav 3 oncogene 497498  48 . . . 2591 OV25 WFDC2: Epididymis-specific, whey-acidic protein499 500 28 . . . 405 type, four-disulfide core M197 XBP1: X-box bindingprotein 1, variant 1 501 502 49 . . . 834 M244 XBP1: X-box bindingprotein 1, variant 2 503 504 49 . . . 834

TABLE 6 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M83 AKR1C1:aldo-keto reductase family 1, member C1 3 4  7 . . . 978 (20-alpha(3-alpha)-hydroxysteroid dehydrogenase) M84 AKR1C3: aldo-keto reductasefamily 1, member C3 5 6  1 . . . 972 (3-alpha hydroxysteroiddehydrogenase, type II) M86 AQP3: Aquaporin 3, variant 1 9 10 65 . . .943 M87 AQP3: Aquaporin 3, variant 2 11 10 65 . . . 943 M391 ARHGEF12:Rho guanine exchange factor (GEF) 14 15  8 . . . 4642 12 M672 ASS:argininosuccinate synthetase, transcript 16 17  76 . . . 1314 variant 1M673 ASS: argininosuccinate synthetase, transcript 18 19  81 . . . 1319variant 2 M200 ATP5A1: ATP synthase, H+ transporting, 20 21  59 . . .1720 mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscleM392 BAK1: BCL2-antagonist/killer 1 24 25 201 . . . 836  M394 C1orf21:chromosome 1 open reading frame 21 32 33 400 . . . 765  M202 CALM1:calmodulin 1 (phosphorylase kinase, delta) 34 35 200 . . . 649  M367CD24: CD24 antigen (small cell lung carcinoma 38 39 57 . . . 299 cluster4 antigen) M95 CDC2: cell division cycle 2, G1 to S and G2 to M 40 41127 . . . 1020 M254 CGI-96: CGI-96 protein 52 53 175 . . . 1146 M104CrkRS: CDC2-related protein kinase 7 85 86  34 . . . 4506 M395 CSK:c-src tyrosine kinase 87 88 413 . . . 1765 M396 CYP1B1: cytochrome P450,subfamily I (dioxin- 95 96 373 . . . 2004 inducible), polypeptide 1 M106CYP24: cytochrome P450, subfamily XXIV (vitamin 97 98 405 . . . 1946 D24-hydroxylase) M109 DKFZP564D206: hypothetical protein 107 108 <1 . . .405 DKFZP564D206 M112 DRIL1: dead ringer (Drosophila)-like 1 117 118 201. . . 1982 M211 ENO1: enolase 1, (alpha) 123 124  95 . . . 1399 M113ERBB2: v-erb-b2 avian erythroblastic leukemia viral 125 126 151 . . .3919 oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)M114 ESR1: estrogen receptor 1 127 128 361 . . . 2148 M115 F2R:coagulation factor II (thrombin) receptor 129 130 345 . . . 1622 M116FABP7: B-FABP, fatty acid binding protein 7 131 132 77 . . . 475 M117FACL2: fatty-acid-Coenzyme A ligase, long-chain 2 133 134  14 . . . 2110M397 FGF7: fibroblast growth factor 7 (keratinocyte 137 138 446 . . .1030 growth factor) M514 FLJ20940: hypothetical protein FLJ20940 153 154236 . . . 742  M399 FLJ21174: hypothetical protein FLJ21174 155 156 234. . . 881  M400 FLJ22418: hypothetical protein FLJ22418 163 164 71 . . .919 M215 GABRP: gamma-aminobutyric acid (GABA) A 171 172 157 . . . 1479receptor, pi M128 GATA2: GATA-binding protein 2 173 174 194 . . . 1618M216 GATA3: GATA-binding protein 3, variant 1 175 176 461 . . . 1792M217 GATA3: GATA-binding protein 3, variant 2 177 176 461 . . . 1792M218 GATA3: GATA-binding protein 3, variant 3 178 176 152 . . . 1483M129 GNLY: granulysin, isoform 519 179 180 281 . . . 670  M130 GNLY:granulysin, isoform NKG5 181 182 129 . . . 566  M131 GPI: glucosephosphate isomerase 187 188  16 . . . 1692 M495 GSTP1: glutathioneS-transferase pi 191 192 30 . . . 662 M220 GUCY1A3: guanylate cyclase 1,soluble, alpha 3, 193 194 520 . . . 2592 variant 1 M221 GUCY1A3:guanylate cyclase 1, soluble, alpha 3, 195 194 386 . . . 2458 variant 2M222 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 196 194 407 . . .2479 variant 3 M133 GZMA: Granzyme A (Cytotoxic T-lymphocyte- 197 198 39. . . 827 associated serine esterase-3; Hanukah factor serine protease);CTL tryptase M196 HAG-3: anterior gradient protein 3, variant 1 201 20249 . . . 549 M134 HDAC2: histone deacetylase 2 205 206 205 . . . 1671M273 HMGCS2: 3-hydroxy-3-methylglutaryl-Coenzyme A 207 208  52 . . .1578 synthase 2 (mitochondrial) M674 HN1: hematological and neurologicalexpressed 1 209 210 104 . . . 568  M136 HPD: 4-hydroxyphenylpyruvatedioxygenase 215 216  26 . . . 1207 M137 HPGD: hydroxyprostaglandindehydrogenase 15- 217 218 18 . . . 818 (NAD) M401 HSCP1: serinecarboxypeptidase 1 precursor 219 220  33 . . . 1391 protein M402 HSPD1:heat shock 60 kD protein 1 (chaperonin) 223 224  25 . . . 1746 M139IGSF1: IGCD1, IGDC1, KIAA036, immunoglobulin 227 228  81 . . . 4091superfamily, member 1 M404 IL6ST: interleukin 6 signal transducer(gp130, 229 230 256 . . . 3012 oncostatin M receptor) M144 KIAA1277:KIAA1277 protein 251 252  <5 . . . 3079 M145 KIAA1361: KIAA1361 protein253 254 <141 . . . 3158  M148 LBP: lipopolysaccharide-binding protein259 260  18 . . . 1463 M229 LDHB: lactate dehydrogenase B 261 262  85 .. . 1089 M558 LOC118430: small breast epithelial mucin 265 266 69 . . .341 M406 LOC51242: hypothetical protein LOC51242 267 268  1 . . . 435M230 LOC57402: S100-type calcium binding protein A14 269 270 99 . . .413 M152 MDS024: MDS024 protein 273 274 65 . . . 838 M153 ME1: malicenzyme 1, NADP(+)-dependent, 275 276 108 . . . 1826 cytosolic M675MGC9753: hypothetical protein MGC9753 289 290 1092 . . . 1814  M156 MIG:monokine induced by gamma interferon 293 294 40 . . . 417 M157 MLN64:steroidogenic acute regulatory protein 295 296 122 . . . 1459 relatedM158 MMP11: matrix metalloproteinase 11 preproprotein; 297 298  23 . . .1489 stromelysin 3 OV52 MMP7: matrix metalloproteinase 7 (matrilysin,299 300 28 . . . 831 uterine) M407 MS4A7: membrane-spanning 4-domains,subfamily 301 302 147 . . . 869  A, member 7, variant 1 M676 MS4A7:membrane-spanning 4-domains, subfamily 303 302 118 . . . 840  A, member7, variant 2 M150 MSC: mitochondrial solute carrier, hypothetical 304305 368 . . . 652  protein PRO1278; HT015 protein M151 MST4:serine/threonine protein kinase MASK 306 307 118 . . . 1368 M159 MTHFD2:methylene tetrahydrofolate 308 309  16 . . . 1050 dehydrogenase (NAD+dependent), methenyltetrahydrofolate cyclohydrolase M669 MUC1: mucin 1,transmembrane 310 311  74 . . . 3841 M233 MYO5A: myosin VA (heavypolypeptide 12, myoxin) 314 315 251 . . . 5818 M162 NAT1:N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M163 NAT1: N-acetyltransferase 1 (arylamine N- 320319 441 . . . 1313 acetyltransferase), NAT1*11B allele M677 NCALD:neurocalcin delta 321 322 121 . . . 702  M408 NDRG1: N-myc downstreamregulated protein 323 324 111 . . . 1295 M165 NPY1R: neuropeptide Yreceptor Y1 329 330 209 . . . 1363 OV48 OPN-a: Secreted phosphoprotein-1(osteopontin, 335 336  1 . . . 942 bone sialoprotein) OV49 OPN-b:Secreted phosphoprotein-1 (osteopontin, 337 338 88 . . . 990 bonesialoprotein) OV50 OPN-c: Secreted phosphoprotein-1 (osteopontin, 339340  1 . . . 861 bone sialoprotein) M170 PPARBP, PPAR binding protein,thyroid hormone 365 366 236 . . . 4936 receptor interactor 2; PPARGbinding protein M171 PPIF: peptidylprolyl isomerase F (cyclophilin F),367 368 72 . . . 695 variant 1 M173 PPIF: peptidylprolyl isomerase F(cyclophilin F), 370 371 84 . . . 659 variant 3 M177 PROML1: prominin(mouse)-like 1; hematopoietic 376 377  38 . . . 2635 stem cell antigenM237 PSMB3: proteasome (prosome, macropain) subunit, 378 379 18 . . .635 beta type, 3 M678 PSMB9: proteasome (prosome, macropain) subunit,380 381 41 . . . 700 beta type, 9 (large multifunctional protease 2)M178 PSMD3: proteasome (prosome, macropain) 26S 382 383 158 . . . 1762subunit, non-ATPase, 3 M180 RAMP3: receptor (calcitonin) activitymodifying 392 393 30 . . . 476 protein 3 precursor; calcitoninreceptor-like receptor activity modifying protein 3 M679 RARRES1:retinoic acid receptor responder 394 395 37 . . . 723 (tazaroteneinduced) 1, variant 1 M680 RARRES1: retinoic acid receptor responder 396397 128 . . . 1012 (tazarotene induced) 1, variant 2 M91 RASGRP1: RASguanyl releasing protein 1 (calcium 398 399  <1 . . . 2351 andDAG-regulated) M418 RNB6: RNB6 protein, variant 2 402 403 125 . . . 1285M181 RPL19: ribosomal protein L19 404 405 29 . . . 619 M182 RQCD1: rcd1(required for cell differentiation, 406 407  1 . . . 900 S. pombe)homolog 1 M183 S100A8: S100 calcium-binding protein A8 408 409 56 . . .340 M239 SCD: stearoyl-CoA desaturase (delta-9-desaturase) 410 411 236 .. . 1315 M421 SERHL: kraken-like, variant 1 416 417 118 . . . 1062 M422SERHL: kraken-like, variant 2 418 419 82 . . . 693 M185 SLPI: secretoryleukocyte protease inhibitor 429 430 19 . . . 417 (antileukoproteinase),variant 1 M681 SLPI: secretory leukocyte protease inhibitor 431 430 23 .. . 421 (antileukoproteinase), variant 2 M424 STAT4: signal transducerand activator of 436 437  82 . . . 1353 transcription 4, variant 1 M425STAT4: signal transducer and activator of 438 439  82 . . . 2328transcription 4, variant 2 M187 STC1: stanniocalcin 1 440 441 285 . . .1028 M189 TAF1C: TATA box binding protein (TBP)-associated 452 453 185 .. . 2794 factor, RNA polymerase I, C, 110 kD M242 TFF1: trefoil factor 1(breast cancer, estrogen- 463 464 41 . . . 295 inducible sequenceexpressed in) M191 TLN1: talin 1 469 470 127 . . . 7752 M427 UGDH:UDP-glucose dehydrogenase 473 474  79 . . . 1563 M194 unnamed gene (2)477 478  23 . . . 1066 M234 unnamed gene (3) 479 480 55 . . . 676 M393unnamed gene (4) 481 482 287 . . . 406  M198 ZNF217: zinc finger protein217 505 506 272 . . . 3418

TABLE 7 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M114 ESR1:estrogen receptor 1 127 128 361 . . . 2148 M216 GATA3: GATA-bindingprotein 3, variant 1 175 176 461 . . . 1792 M217 GATA3: GATA-bindingprotein 3, variant 2 177 176 461 . . . 1792 M218 GATA3: GATA-bindingprotein 3, variant 3 178 176 152 . . . 1483 M196 HAG-3: anteriorgradient protein 3, variant 1 201 202 49 . . . 549 M156 MIG: monokineinduced by gamma interferon 293 294 40 . . . 417 M158 MMP11: matrixmetalloproteinase 11 preproprotein; 297 298  23 . . . 1489 stromelysin 3M162 NAT1: N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M163 NAT1: N-acetyltransferase 1 (arylamine N- 320319 441 . . . 1313 acetyltransferase), NAT1*11B allele M165 NPY1R:neuropeptide Y receptor Y1 329 330 209 . . . 1363 OV48 OPN-a: Secretedphosphoprotein-1 (osteopontin, 335 336  1 . . . 942 bone sialoprotein)OV49 OPN-b: Secreted phosphoprotein-1 (osteopontin, 337 338 88 . . . 990bone sialoprotein) OV50 OPN-c: Secreted phosphoprotein-1 (osteopontin,339 340  1 . . . 861 bone sialoprotein) M242 TFF1: trefoil factor 1(breast cancer, estrogen- 463 464 41 . . . 295 inducible sequenceexpressed in) M427 UGDH: UDP-glucose dehydrogenase 473 474  79 . . .1563 M194 unnamed gene (2) 477 478  23 . . . 1066

TABLE 8 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M394C1orf21: chromosome 1 open reading frame 21 32 33 400 . . . 765  M106CYP24: cytochrome P450, subfamily XXIV (vitamin 97 98 405 . . . 1946 D24-hydroxylase) M112 DRIL1: dead ringer (Drosophila)-like 1 117 118 201. . . 1982 M114 ESR1: estrogen receptor 1 127 128 361 . . . 2148 M399FLJ21174: hypothetical protein FLJ21174 155 156 234 . . . 881  M400FLJ22418: hypothetical protein FLJ22418 163 164 71 . . . 919 M216 GATA3:GATA-binding protein 3, variant 1 175 176 461 . . . 1792 M217 GATA3:GATA-binding protein 3, variant 2 177 176 461 . . . 1792 M218 GATA3:GATA-binding protein 3, variant 3 178 176 152 . . . 1483 M220 GUCY1A3:guanylate cyclase 1, soluble, alpha 3, 193 194 520 . . . 2592 variant 1M221 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 195 194 386 . . .2458 variant 2 M222 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 196194 407 . . . 2479 variant 3 M273 HMGCS2:3-hydroxy-3-methylglutaryl-Coenzyme A 207 208  52 . . . 1578 synthase 2(mitochondrial) M136 HPD: 4-hydroxyphenylpyruvate dioxygenase 215 216 26 . . . 1207 M137 HPGD: hydroxyprostaglandin dehydrogenase 15- 217 21818 . . . 818 (NAD) M404 IL6ST: interleukin 6 signal transducer (gp130,229 230 256 . . . 3012 oncostatin M receptor) M229 LDHB: lactatedehydrogenase B 261 262  85 . . . 1089 M676 MS4A7: membrane-spanning4-domains, subfamily 303 302 118 . . . 840  A, member 7, variant 2 M162NAT1: N-acetyltransferase 1 (arylamine N- 318 319  1 . . . 873acetyltransferase) M163 NAT1: N-acetyltransferase 1 (arylamine N- 320319 441 . . . 1313 acetyltransferase), NAT1*11B allele M677 NCALD:neurocalcin delta 321 322 121 . . . 702  M91 RASGRP1: RAS guanylreleasing protein 1 (calcium 398 399  <1 . . . 2351 and DAG-regulated)M418 RNB6: RNB6 protein, variant 2 402 403 125 . . . 1285 M182 RQCD1:rcd1 (required for cell differentiation, 406 407  1 . . . 900 S. pombe)homolog 1 M189 TAF1C: TATA box binding protein (TBP)-associated 452 453185 . . . 2794 factor, RNA polymerase I, C, 110 kD M242 TFF1: trefoilfactor 1 (breast cancer, estrogen- 463 464 41 . . . 295 induciblesequence expressed in) M427 UGDH: UDP-glucose dehydrogenase 473 474  79. . . 1563 M194 unnamed gene (2) 477 478  23 . . . 1066 M393 unnamedgene (4) 481 482 287 . . . 406  M198 ZNF217: zinc finger protein 217 505506 272 . . . 3418

TABLE 9 SEQ ID SEQ ID Marker Gene Name NO (nts) NO (AAs) CDS M83 AKR1C1:aldo-keto reductase family 1, member C1 3 4  7 . . . 978 (20-alpha(3-alpha)-hydroxysteroid dehydrogenase) M84 AKR1C3: aldo-keto reductasefamily 1, member C3 5 6  1 . . . 972 (3-alpha hydroxysteroiddehydrogenase, type II) M86 AQP3: Aquaporin 3, variant 1 9 10 65 . . .943 M87 AQP3: Aquaporin 3, variant 2 11 10 65 . . . 943 M391 ARHGEF12:Rho guanine exchange factor (GEF) 14 15  8 . . . 4642 12 M672 ASS:argininosuccinate synthetase, transcript 16 17  76 . . . 1314 variant 1M673 ASS: argininosuccinate synthetase, transcript 18 19  81 . . . 1319variant 2 M200 ATP5A1: ATP synthase, H+ transporting, 20 21  59 . . .1720 mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscleM392 BAK1: BCL2-antagonist/killer 1 24 25 201 . . . 836  M202 CALM1:calmodulin 1 (phosphorylase kinase, 34 35 200 . . . 649  delta) M367CD24: CD24 antigen (small cell lung carcinoma 38 39 57 . . . 299 cluster4 antigen) M95 CDC2: cell division cycle 2, G1 to S and G2 to M 40 41127 . . . 1020 M254 CGI-96: CGI-96 protein 52 53 175 . . . 1146 M104CrkRS: CDC2-related protein kinase 7 85 86  34 . . . 4506 M395 CSK:c-src tyrosine kinase 87 88 413 . . . 1765 M396 CYP1B1: cytochrome P450,subfamily I (dioxin- 95 96 373 . . . 2004 inducible), polypeptide 1 M109DKFZP564D206: hypothetical protein 107 108 <1 . . . 405 DKFZP564D206M211 ENO1: enolase 1, (alpha) 123 124  95 . . . 1399 M113 ERBB2:v-erb-b2 avian erythroblastic leukemia 125 126 151 . . . 3919 viraloncogene homolog 2 (neuro/glioblastoma derived oncogene homolog) M115F2R: coagulation factor II (thrombin) receptor 129 130 345 . . . 1622M116 FABP7: B-FABP, fatty acid binding protein 7 131 132 77 . . . 475M117 FACL2: fatty-acid-Coenzyme A ligase, long-chain 2 133 134  14 . . .2110 M397 FGF7: fibroblast growth factor 7 (keratinocyte 137 138 446 . .. 1030 growth factor) M514 FLJ20940: hypothetical protein FLJ20940 153154 236 . . . 742  M215 GABRP: gamma-aminobutyric acid (GABA) A 171 172157 . . . 1479 receptor, pi M128 GATA2: GATA-binding protein 2 173 174194 . . . 1618 M129 GNLY: granulysin, isoform 519 179 180 281 . . . 670 M130 GNLY: granulysin, isoform NKG5 181 182 129 . . . 566  M131 GPI:glucose phosphate isomerase 187 188  16 . . . 1692 M495 GSTP1:glutathione S-transferase pi 191 192 30 . . . 662 M133 GZMA: Granzyme A(Cytotoxic T-lymphocyte- 197 198 39 . . . 827 associated serineesterase-3; Hanukah factor serine protease); CTL tryptase M196 HAG-3:anterior gradient protein 3, variant 1 201 202 49 . . . 549 M134 HDAC2:histone deacetylase 2 205 206 205 . . . 1671 M674 HN1: hematological andneurological expressed 1 209 210 104 . . . 568  M401 HSCP1: serinecarboxypeptidase 1 precursor 219 220  33 . . . 1391 protein M402 HSPD1:heat shock 60 kD protein 1 (chaperonin) 223 224  25 . . . 1746 M139IGSF1: IGCD1, IGDC1, KIAA036, immunoglobulin 227 228  81 . . . 4091superfamily, member 1 M144 KIAA1277: KIAA1277 protein 251 252  <5 . . .3079 M145 KIAA1361: KIAA1361 protein 253 254 <141 . . . 3158  M148 LBP:lipopolysaccharide-binding protein 259 260  18 . . . 1463 M558LOC118430: small breast epithelial mucin 265 266 69 . . . 341 M406LOC51242: hypothetical protein LOC51242 267 268  1 . . . 435 M230LOC57402: S100-type calcium binding protein A14 269 270 99 . . . 413M152 MDS024: MDS024 protein 273 274 65 . . . 838 M153 ME1: malic enzyme1, NADP(+)-dependent, 275 276 108 . . . 1826 cytosolic M675 MGC9753:hypothetical protein MGC9753 289 290 1092 . . . 1814  M156 MIG: monokineinduced by gamma interferon 293 294 40 . . . 417 M157 MLN64:steroidogenic acute regulatory protein 295 296 122 . . . 1459 relatedM158 MMP11: matrix metalloproteinase 11 297 298  23 . . . 1489preproprotein; stromelysin 3 OV52 MMP7: matrix metalloproteinase 7(matrilysin, 299 300 28 . . . 831 uterine) M407 MS4A7: membrane-spanning4-domains, subfamily 301 302 147 . . . 869  A, member 7, variant 1 M150MSC: mitochondrial solute carrier, hypothetical 304 305 368 . . . 652 protein PRO1278; HT015 protein M151 MST4: serine/threonine proteinkinase MASK 306 307 118 . . . 1368 M159 MTHFD2: methylenetetrahydrofolate 308 309  16 . . . 1050 dehydrogenase (NAD+ dependent),methenyltetrahydrofolate cyclohydrolase M669 MUC1: mucin 1,transmembrane 310 311  74 . . . 3841 M233 MYO5A: myosin VA (heavypolypeptide 12, 314 315 251 . . . 5818 myoxin) M408 NDRG1: N-mycdownstream regulated protein 323 324 111 . . . 1295 M165 NPY1R:neuropeptide Y receptor Y1 329 330 209 . . . 1363 OV48 OPN-a: Secretedphosphoprotein-1 (osteopontin, 335 336  1 . . . 942 bone sialoprotein)OV49 OPN-b: Secreted phosphoprotein-1 (osteopontin, 337 338 88 . . . 990bone sialoprotein) OV50 OPN-c: Secreted phosphoprotein-1 (osteopontin,339 340  1 . . . 861 bone sialoprotein) M170 PPARBP, PPAR bindingprotein, thyroid hormone 365 366 236 . . . 4936 receptor interactor 2;PPARG binding protein M171 PPIF: peptidylprolyl isomerase F (cyclophilinF), 367 368 72 . . . 695 variant 1 M173 PPIF: peptidylprolyl isomerase F(cyclophilin F), 370 371 84 . . . 659 variant 3 M177 PROML1: prominin(mouse)-like 1; hematopoietic 376 377  38 . . . 2635 stem cell antigenM237 PSMB3: proteasome (prosome, macropain) 378 379 18 . . . 635subunit, beta type, 3 M678 PSMB9: proteasome (prosome, macropain) 380381 41 . . . 700 subunit, beta type, 9 (large multifunctional protease2) M178 PSMD3: proteasome (prosome, macropain) 26S 382 383 158 . . .1762 subunit, non-ATPase, 3 M180 RAMP3: receptor (calcitonin) activitymodifying 392 393 30 . . . 476 protein 3 precursor; calcitoninreceptor-like receptor activity modifying protein 3 M679 RARRES1:retinoic acid receptor responder 394 395 37 . . . 723 (tazaroteneinduced) 1, variant 1 M680 RARRES1: retinoic acid receptor responder 396397 128 . . . 1012 (tazarotene induced) 1, variant 2 M181 RPL19:ribosomal protein L19 404 405 29 . . . 619 M183 S100A8: S100calcium-binding protein A8 408 409 56 . . . 340 M239 SCD: stearoyl-CoAdesaturase (delta-9- 410 411 236 . . . 1315 desaturase) M421 SERHL:kraken-like, variant 1 416 417 118 . . . 1062 M422 SERHL: kraken-like,variant 2 418 419 82 . . . 693 M185 SLPI: secretory leukocyte proteaseinhibitor 429 430 19 . . . 417 (antileukoproteinase), variant 1 M681SLPI: secretory leukocyte protease inhibitor 431 430 23 . . . 421(antileukoproteinase), variant 2 M424 STAT4: signal transducer andactivator of 436 437  82 . . . 1353 transcription 4, variant 1 M425STAT4: signal transducer and activator of 438 439  82 . . . 2328transcription 4, variant 2 M187 STC1: stanniocalcin 1 440 441 285 . . .1028 M191 TLN1: talin 1 469 470 127 . . . 7752 M234 unnamed gene (3) 479480 55 . . . 676

TABLE 10 SEQ ID SEQ ID NO NO Marker Gene Name (nts) (AAs) CDS M553CLECSF-1: C-type (calcium dependent, 56 57 53 . . . 673carbohydrate-recognition domain) lectin, superfamily member 1(cartilage-derived), variant 2 OV66 CP: ceruloplasmin (ferroxidase),variant 3 79 80  1 . . . 3210 M554 DKFZP566I133: hypothetical protein113 114 134 . . . 1354 DKFZp566I133, variant 2 M120 FLJ12425:hypothetical protein FLJ12425 143 144 42 . . . 335 M220 GUCY1A3:guanylate cyclase 1, soluble, alpha 3, 193 194 520 . . . 2592 variant 1M221 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 195 194 386 . . .2458 variant 2 M222 GUCY1A3: guanylate cyclase 1, soluble, alpha 3, 196194 407 . . . 2479 variant 3 M225 HAG-3: anterior gradient protein 3,variant 2 203 204 116 . . . 129  M405 KIAA1077: KIAA1077 protein 247 248267 . . . 2882 M236 NY-BR-1.1: breast cancer antigen NY-BR-1.1 331 332181 . . . 3858 M173 PPIF: peptidylprolyl isomerase F (cyclophilin F),370 371 84 . . . 659 variant 3 M680 RARRES1: retinoic acid receptorresponder 396 397 128 . . . 1012 (tazarotene induced) 1, variant 2 M418RNB6: RNB6 protein, variant 2 402 403 125 . . . 1285 M423 SQLE: squaleneepoxidase 434 435 876 . . . 2600 M424 STAT4: signal transducer andactivator of 436 437  82 . . . 1353 transcription 4, variant 1 M565SYTL2: synaptotagmin-like 2 446 447 261 . . . 1766 M620 TFAP2B:transcription factor AP-2 beta (activating 459 460 257 . . . 1639enhancer binding protein 2 beta), variant 1 M621 TFAP2B: transcriptionfactor AP-2 beta (activating 461 462 257 . . . 1666 enhancer bindingprotein 2 beta), variant 2 M193 unnamed gene (1) 475 476  75 . . . 1697M194 unnamed gene (2) 477 478  23 . . . 1066 M234 unnamed gene (3) 479480 55 . . . 676 M428 unnamed gene (6), variant 1 485 486  75 . . . 2471M429 unnamed gene (6), variant 2 487 488  75 . . . 1535 M622 unnamedgene (7) 489 490 579à803 M93 unnamed gene (CASB619), variant 1 491 492310 . . . 3351 M94 unnamed gene (CASB619), variant 2 493 494 310 . . .3324

TABLE 11 SEQ ID SEQ ID NO NO Marker Gene Name (nts) (AAs) CDS M86 AQP3:Aquaporin 3, variant 1 9 10 65 . . . 943 M205 COL12A1: collagen, typeXII, alpha 1, variant 1 60 61  1 . . . 9192 M618 COL12A1: collagen, typeXII, alpha 1, variant 2 62 63 114 . . . 9305 M555 DUSP4: dualspecificity phosphatase 4 119 120 502 . . . 1686 M216 GATA3:GATA-binding protein 3, variant 1 175 176 461 . . . 1792 M217 GATA3:GATA-binding protein 3, variant 2 177 176 461 . . . 1792 M227 KIAA0878:KIAA0878 protein 241 242 336 . . . 2171 M407 MS4A7: membrane-spanning4-domains, subfamily 301 302 147 . . . 869  A, member 7, variant 1 M561NDUFA8: NADH dehydrogenase (ubiquinone) 1 325 326 68 . . . 586 alphasubcomplex, 8 (19 kD, PGIV) M421 SERHL: kraken-like, variant 1 416 417118 . . . 1062 M619 SIAH2: seven in absentia (Drosophila) homolog 2, 426425 527 . . . 1501 variant 2 M568 TFAP2A: transcription factor AP-2alpha (activating 456 457 282 . . . 1601 enhancer-binding protein 2alpha), variant 1 M569 TFAP2A: transcription factor AP-2 alpha(activating 458 457 282 . . . 1601 enhancer-binding protein 2 alpha),variant 2

TABLE 12 SEQ ID NO SEQ ID NO Marker Gene Name (nts) (AA) M82 AF245505,adlican mRNA, complete cds 109 110 M113 ERBB2, v-erb-b2 avianerythroblastic leukemia viral 125 126 oncogene homolog 2(neuro/glioblastoma derived oncogene homolog); M116 FABP7, B-FABP, fattyacid binding protein 7, brain; 131 132 M130 GNLY, granulysin, isoformNKG5 181 182 M157 MLN64, steroidogenic acute regulatory protein related295 296 M170 PPARBP, PPAR binding protein, thyroid hormone 365 366receptor interactor 2; PPARG binding protein M171 PPIF, peptidylprolylisomerase F (cyclophilin F), variant 1 367 368 M173 PPIF, peptidylprolylisomerase F (cyclophilin F), variant 3 370 371 M180 RAMP3, receptor(calcitonin) activity modifying protein 3 392 393 precursor; calcitoninreceptor-like receptor activity modifying protein 3 M183 S100A8, S100calcium-binding protein A8; 60B8AG 408 409 M185 SLPI, secretoryleukocyte protease inhibitor 429 430 (antileukoproteinase)

1. A method of assessing whether a patient is afflicted with breastcancer, the method comprising: a) determining the level of expression ofa marker in a patient sample, wherein the marker is selected from thegroup consisting of the markers listed in Table 1; b) determining thelevel of expression of the marker in a control sample; and c) comparingthe level of expression of the marker in the patient sample and thelevel of expression of the marker in the control sample, wherein adifference between the level of expression of the marker in the patientsample as compared to the level of expression of the marker in thecontrol sample is an indication that the patient is afflicted withbreast cancer.
 2. The method of claim 1, wherein the control samplecomprises breast cells from the patient which are non-cancerous.
 3. Themethod of claim 1, wherein the level of expression of the marker in thecontrol sample is predetermined using an average of the levels ofexpression of the marker in samples from a population of subjects havingindolent breast tumors or no breast tumors.
 4. The method of claim 1,wherein the patient sample comprises cells obtained from the patient. 5.The method of claim 1, wherein the patient sample comprises a fluidselected from the group consisting of blood fluid, lymph, cystic fluid,nipple aspirates, and fluid collected from a lump biopsy.
 6. The methodof claim 1, wherein the level of expression of the marker in the patientsample is assessed by detecting the presence of a marker protein in thesample.
 7. The method of claim 6, wherein the presence of the markerprotein is detected using a reagent which specifically binds with theprotein.
 8. The method of claim 7, wherein the reagent is selected fromthe group consisting of an antibody, an antibody derivative, anantigen-binding antibody fragment, and a non-antibody peptide whichspecifically binds the protein.
 9. The method of claim 8, wherein theantibody or antigen-binding antibody fragment is a monoclonal antibodyor antigen-binding fragment thereof, or a polyclonal antibody orantigen-binding fragment thereof.
 10. The method of claim 8, wherein theantibody or antigen-binding antibody fragment is labelled.
 11. Themethod of claim 10, wherein the antibody or antigen-binding antibodyfragment is radio-labelled, biotin-labelled, chromophore labelled,fluorophore labelled, or enzyme labelled.
 12. The method of claim 1,wherein the marker comprises a transcribed polynucleotide or portionthereof.
 13. The method of claim 12, wherein the transcribedpolynucleotide is a mRNA or a cDNA.
 14. The method of claim 12, whereinthe step of detecting a transcribed polynucleotide further comprisesamplifying the transcribed polynucleotide.
 15. The method of claim 1,wherein the level of expression of the marker in the patient sample isassessed by detecting the presence in the patient sample of atranscribed polynucleotide which anneals with a nucleic acid marker or aportion thereof under stringent hybridization conditions.
 16. The methodof claim 1, wherein the level of expression of the marker in the patientsample differs from the level of expression of the marker in the controlsample by a factor selected from the group consisting of: a factor of atleast about 2, a factor of at least about 3, a factor of at least about4, and a factor of at least about
 5. 17. The method of claim 1, whereinthe level of expression of the marker in the patient sample is assessedusing a technique selected from the group consisting of: Northernhybridization, polymerase chain reaction analysis, RT-PCR, probe arrayand in situ hybridization.
 18. The method of claim 1, furthercomprising: d) determining the level of expression in the patient sampleof each of a plurality of markers independently selected from themarkers listed in Table 1: e) determining the level of expression ofeach of the plurality of markers in the control sample; and f) comparingthe level of expression of each of the plurality of markers in thepatient sample and the level of expression of each of the plurality ofmarkers in the control sample, wherein a difference in the level ofexpression of more than one of the markers in the patient sample ascompared to the corresponding level of expression of the markers in thecontrol sample is an indication that the patient is afflicted withbreast cancer.
 19. The method of claim 18, wherein the level ofexpression of at least three markers or at least five markers isdetermined.
 20. A method for assessing whether a patient has breastcancer that has metastasized or is likely to metastasize, comprising: a)determining the level of expression of a marker in a patient sample,wherein the marker is selected from the markers listed in Table 1, b)determining the level of expression of the marker in a control sample,and c) comparing the level of expression of the marker in the patientsample and the level of expression of the marker in the control sample;wherein a higher level of expression in the patient sample as comparedto the level of expression of the marker in the control sample is anindication that the breast cancer has metastasized or is likely tometastasize.
 21. The method of claim 20, wherein the assessment isindicative of whether the patient is afflicted with metastatic breastcancer that has metastasized to lymph nodes, or is likely to metastasizeto lymph nodes.
 22. A method for predicting the clinical outcome of abreast cancer patient, the method comprising: a) determining the levelof expression of a marker in a patient sample, wherein the marker isselected from the markers listed in Table 1, b) determining the level ofexpression of the marker in a sample from a control subject having agood clinical outcome; and c) comparing the level of expression of themarker in the patient sample and the level of expression of the markerin the sample from the control subject; wherein a higher level ofexpression of the marker in the patient sample as compared to the levelof expression of the marker in the sample from the control subject is anindication that the patient has a poor clinical outcome.
 23. A methodfor monitoring the progression of breast cancer in a patient, the methodcomprising: a) determining the level of expression of a marker in apatient sample from a first point in time, wherein the marker isselected from the group consisting of the markers listed in Table 1; b)determining the level of expression of the marker in a sample from thepatient at a subsequent point in time; and c) comparing the level ofexpression detected in steps a) and b), thereby monitoring theprogression of breast cancer in the patient, wherein a change in thelevel of expression of the marker is indicative of either progression orregression of breast cancer.
 24. The method of claim 23, wherein thefirst and second samples are portions of a single sample obtained fromthe patient, or portions of pooled samples obtained from the patient.25. A method of assessing the efficacy of a therapy for inhibitingbreast cancer in a patient, the method comprising: a) determining thelevel of expression of a marker in a first sample obtained from thepatient prior to administering at least a portion of the therapy to thepatient, wherein the marker is selected from the group consisting of themarkers listed in Table 1, b) determining the level of expression of themarker in a second sample obtained from the patient subsequent toadministering the portion of the therapy; c) comparing the level ofexpression of the marker in the first sample as compared to the level ofexpression of the marker in the second sample; and d) determining thatthe therapy is efficacious for inhibiting breast cancer in the patientwhen there is a lower level of expression of the marker in the secondsample, relative to the first sample.
 23. A kit for assessing whether apatient is afflicted with breast cancer, the kit comprising reagentssuitable for performing the method of claim 1 and instructions for use.27. An isolated nucleic acid molecule comprising a nucleotide sequenceselected from Tables 10 and
 11. 28. A vector which contains the nucleicacid molecule of claim
 27. 29. A host cell which contains the nucleicacid molecule of claim
 27. 30. An isolated polypeptide comprising anamino acid sequence selected from Table
 10. 31. An antibody whichselectively binds to the polypeptide of claim 30.